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3dll

The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning

Method: X-RAY DIFFRACTION Dmax: 229.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

50S ribosomal protein L2

OrganismNot specified

UniProt Q9RXJ9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain A； UniProt 2–275 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain A 1–274（274 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain A 2–275（274 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain A 2–275（274 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain A 1–275（275 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain A 1–274（274 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain A 2–275（274 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain A 2–275（274 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain A 2–275（274 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–275（275 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain A 2–275（274 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain A 1–275（275 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 1–275（275 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 2–272（271 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 2–275（274 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain A 2–272（271 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL2_DEIRA
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–274； UniProt 2–275

50S ribosomal protein L3

OrganismNot specified

UniProt Q9RXK2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain B； UniProt 1–211 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–211（211 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–211（211 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–211（211 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain B 1–211（211 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–211（211 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2OGM The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-571519 Deposited 2007-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 1–211（211 aa）
Not recorded G19 (2S,3AR,4R,5S,6S,8R,9R,9AR,10R)-2,5-DIHYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROP[1]ENOCYCLOPENTA[8]ANNULEN-8-YL [(6-AMINOPYRIDAZIN-3-YL)CARBONYL]CARBAMATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.334
2OGN The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative SB-280080 Deposited 2007-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 1–211（211 aa）
Not recorded G80 (3AS,4R,5S,6S,8R,9R,9AR,10R)-5-HYDROXY-4,6,9,10-TETRAMETHYL-1-OXO-6-VINYLDECAHYDRO-3A,9-PROPANOCYCLOPENTA[8]ANNULEN-8-YL (PIPERIDIN-4-YLTHIO)ACETATE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.56 Å R-free 0.338
2OGO The crystal structure of the large ribosomal subunit from Deinococcus radiodurans complexed with the pleuromutilin derivative retapamulin (SB-275833) Deposited 2007-01-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Monomer；Protein × 1 PDB declaration: dimeric
Chain B 1–211（211 aa）
Not recorded G34 Retapamulin × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；Ethanol, Dimethylhexanediol, MgCl2, HEPES, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.66 Å R-free 0.334
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–211（211 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–211（211 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–211（211 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain B 1–211（211 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–211（211 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–211（211 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–211（211 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–211（211 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–211（211 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–211（211 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–211（211 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain B 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain B 1–211（211 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–211（211 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–206（206 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–206（206 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain B 1–206（206 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL3_DEIRA
Isoform —
PDB entities 4
Chains and sequence ranges Author chain B； PDBConstruct 1–211； UniProt 1–211

50S ribosomal protein L4

OrganismNot specified

UniProt Q9RXK1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain C； UniProt 1–205 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1J5A STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA Deposited 2002-03-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain K 1–205（205 aa）
Not recorded CTY CLARITHROMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.323
1JZX Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain K 1–205（205 aa）
Not recorded CLY CLINDAMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol,MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.303
1JZY Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain K 1–205（205 aa）
Not recorded ERY ERYTHROMYCIN A × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.301
1JZZ Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain K 1–205（205 aa）
Not recorded ROX ROXITHROMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.80 Å R-free 0.274
1K01 Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain K 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 3 CLM CHLORAMPHENICOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.321
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain C 1–204（204 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain C 2–205（204 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain C 2–205（204 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain C 1–205（205 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain C 1–204（204 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain C 1–205（205 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain C 1–205（205 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain C 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–205（205 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–205（205 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–205（205 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 2–198（197 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain C 2–198（197 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain C 1–205（205 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–205（205 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 2–198（197 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 1–205（205 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain C 2–196（195 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

28 other PDB entries and 28 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL4_DEIRA
Isoform —
PDB entities 5
Chains and sequence ranges Author chain C； PDBConstruct 1–205； UniProt 1–205

50S ribosomal protein L5

OrganismNot specified

UniProt Q9RXJ0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain D； UniProt 1–180 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain D 1–180（180 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain D 1–180（180 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain D 1–180（180 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain D 1–180（180 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain D 1–180（180 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain D 1–180（180 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain D 1–180（180 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain D 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–180（180 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–180（180 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–180（180 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 3–179（177 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain D 3–179（177 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain D 1–180（180 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 1–180（180 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 3–179（177 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 3–179（177 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain D 2–177（176 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL5_DEIRA
Isoform —
PDB entities 6
Chains and sequence ranges Author chain D； PDBConstruct 1–180； UniProt 1–180

50S ribosomal protein L6

OrganismNot specified

UniProt Q9RSL3

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain E； UniProt 1–185 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain E 1–185（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain E 28–212（185 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain E 28–212（185 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain E 1–212（212 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain E 1–185（185 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain E 1–185（185 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain E 1–185（185 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain E 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–185（185 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–185（185 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain E 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain E 1–185（185 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 5–175（171 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain E 5–175（171 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain E 1–185（185 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain E 1–185（185 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain E 5–175（171 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain E 5–175（171 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain E 5–175（171 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL6_DEIRA
Isoform —
PDB entities 7
Chains and sequence ranges Author chain E； PDBConstruct 1–185； UniProt 1–185

50S ribosomal protein L11

OrganismNot specified

UniProt Q9RSS7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain F； UniProt 1–144 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–144（144 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–144（144 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–144（144 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain G 1–144（144 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–144（144 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain F 1–144（144 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain F 1–144（144 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–144（144 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain F 1–144（144 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–144（144 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–144（144 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–144（144 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–144（144 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–144（144 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 4–144（141 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain F 1–144（144 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain F 1–144（144 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253

17 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL11_DEIRA
Isoform —
PDB entities 8
Chains and sequence ranges Author chain F； PDBConstruct 1–144； UniProt 1–144

50S ribosomal protein L13

OrganismNot specified

UniProt Q9RXY1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain G； UniProt 1–174 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain H 1–174（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain H 1–174（174 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain H 1–174（174 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain H 1–174（174 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain H 1–174（174 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–174（174 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–174（174 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain G 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–174（174 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–174（174 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain G 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain G 1–174（174 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 30–171（142 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain G 30–171（142 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain G 1–174（174 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain G 1–174（174 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain G 30–172（143 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain G 30–172（143 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain G 30–171（142 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL13_DEIRA
Isoform —
PDB entities 9
Chains and sequence ranges Author chain G； PDBConstruct 1–174； UniProt 1–174

50S ribosomal protein L14

OrganismNot specified

UniProt Q9RXJ2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain H； UniProt 1–134 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain I 1–134（134 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain I 1–134（134 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain I 1–134（134 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain I 1–134（134 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain I 1–134（134 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain H 1–134（134 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain H 1–134（134 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain H 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain H 1–134（134 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain H 1–134（134 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain H 1–134（134 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain H 1–134（134 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain H 1–134（134 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL14_DEIRA
Isoform —
PDB entities 10
Chains and sequence ranges Author chain H； PDBConstruct 1–134； UniProt 1–134

50S ribosomal protein L15

OrganismNot specified

UniProt Q9RSK9

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain I； UniProt 1–156 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain J 1–156（156 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain J 1–156（156 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain J 1–156（156 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain J 1–156（156 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain J 1–156（156 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain I 1–156（156 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain I 1–156（156 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain I 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–156（156 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–156（156 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain I 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain I 1–156（156 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 4–144（141 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain I 4–144（141 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain I 1–156（156 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain I 1–156（156 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain I 1–137（137 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain I 1–137（137 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain I 1–137（137 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL15_DEIRA
Isoform —
PDB entities 11
Chains and sequence ranges Author chain I； PDBConstruct 1–156； UniProt 1–156

50S ribosomal protein L16

OrganismNot specified

UniProt Q9RXJ5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain J； UniProt 1–141 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NJM The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin Deposited 2003-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain K 2–142（141 aa）
Not recorded SPS SPARSOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM
Resolution 3.60 Å R-free 0.308
1NJP The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) Deposited 2003-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain K 2–142（141 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM , pH 7.80
Resolution 3.50 Å R-free 0.295
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain K 1–140（140 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain K 2–142（141 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain K 2–142（141 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain K 1–142（142 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain K 2–142（141 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
1Y69 RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2004-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain K 1–141（141 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 3.33 Å R-free 0.338
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain J 1–141（141 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain J 1–141（141 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–141（141 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain J 1–141（141 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–141（141 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–141（141 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–141（141 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–141（141 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 1–141（141 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain J 1–141（141 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain J 1–141（141 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 5–140（136 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain J 5–140（136 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain J 1–141（141 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain J 1–141（141 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain J 5–140（136 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain J 5–140（136 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain J 5–138（134 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

26 other PDB entries and 26 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL16_DEIRA
Isoform —
PDB entities 12
Chains and sequence ranges Author chain J； PDBConstruct 2–142； UniProt 1–141

50S ribosomal protein L17

OrganismNot specified

UniProt Q9RSJ5

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain K； UniProt 1–116 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain L 1–116（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain L 1–116（116 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain L 1–116（116 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain L 1–116（116 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain L 1–116（116 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain K 1–116（116 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain K 1–116（116 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–116（116 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain K 1–116（116 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–116（116 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–116（116 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–116（116 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–116（116 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 1–116（116 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain K 1–116（116 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain K 1–116（116 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 3–115（113 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain K 3–115（113 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain K 1–116（116 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain K 1–116（116 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain K 1–116（116 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain K 1–116（116 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain K 1–115（115 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL17_DEIRA
Isoform —
PDB entities 13
Chains and sequence ranges Author chain K； PDBConstruct 1–116； UniProt 1–116

50S ribosomal protein L18

OrganismNot specified

UniProt Q9RSL2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain L； UniProt 1–114 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 1–113（113 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 2–114（113 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 2–114（113 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain M 1–114（114 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 1–113（113 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain L 1–114（114 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain L 1–114（114 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–114（114 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–114（114 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain L 1–114（114 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 8–111（104 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain L 8–111（104 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain L 1–114（114 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain L 1–114（114 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain L 8–111（104 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain L 8–111（104 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain L 8–111（104 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL18_DEIRA
Isoform —
PDB entities 14
Chains and sequence ranges Author chain L； PDBConstruct 1–114； UniProt 1–114

50S ribosomal protein L19

OrganismNot specified

UniProt Q9RWB4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain M； UniProt 1–166 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain N 1–166（166 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain N 1–166（166 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain N 1–166（166 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain N 1–166（166 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain N 1–166（166 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 1–166（166 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 1–166（166 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–166（166 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain M 1–166（166 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–166（166 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–166（166 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–166（166 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–166（166 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 1–166（166 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 1–166（166 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 2–166（165 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 2–106（105 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain M 2–115（114 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain M 1–166（166 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 1–166（166 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 1–113（113 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 1–166（166 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain M 2–119（118 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL19_DEIRA
Isoform —
PDB entities 15
Chains and sequence ranges Author chain M； PDBConstruct 1–166； UniProt 1–166

50S ribosomal protein L20

OrganismNot specified

UniProt Q9RSW7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain N； UniProt 1–118 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–118（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–118（118 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–118（118 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain O 1–118（118 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–118（118 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain N 1–118（118 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain N 1–118（118 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 1–118（118 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 1–118（118 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 1–118（118 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 2–118（117 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain N 2–118（117 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain N 1–118（118 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 1–118（118 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 2–118（117 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 2–118（117 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain N 2–118（117 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL20_DEIRA
Isoform —
PDB entities 16
Chains and sequence ranges Author chain N； PDBConstruct 1–118； UniProt 1–118

50S ribosomal protein L21

OrganismNot specified

UniProt Q9RY64

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain O； UniProt 1–100 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain P 1–100（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain P 70–169（100 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain P 70–169（100 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain P 70–169（100 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain P 1–100（100 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–100（100 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–100（100 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain O 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–100（100 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–100（100 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–100（100 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 5–98（94 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain O 5–98（94 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain O 1–100（100 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–100（100 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–98（98 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–98（98 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain O 1–98（98 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL21_DEIRA
Isoform —
PDB entities 17
Chains and sequence ranges Author chain O； PDBConstruct 1–100； UniProt 1–100

50S ribosomal protein L22

OrganismNot specified

UniProt Q9RXJ7

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain P； UniProt 1–134 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1J5A STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA Deposited 2002-03-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain L 1–134（134 aa）
Not recorded CTY CLARITHROMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.323
1JZX Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain L 1–134（134 aa）
Not recorded CLY CLINDAMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol,MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.303
1JZY Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain L 1–134（134 aa）
Not recorded ERY ERYTHROMYCIN A × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.301
1JZZ Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain L 1–134（134 aa）
Not recorded ROX ROXITHROMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.80 Å R-free 0.274
1K01 Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain L 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 3 CLM CHLORAMPHENICOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.321
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–134（134 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–134（134 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–134（134 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1OND THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC Deposited 2003-02-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain Q 1–134（134 aa）
Not recorded TAO TROLEANDOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；EVAPORATION
Resolution 3.40 Å R-free 0.310
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain Q 1–134（134 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–134（134 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain P 1–134（134 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain P 1–134（134 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain P 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–134（134 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–134（134 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 1–134（134 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain P 1–134（134 aa）
Mutation：Insertion of VPR after R109 MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain P 1–109（109 aa）
Chain P 110–134（25 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 8–134（127 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain P 8–134（127 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain P 1–134（134 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain P 1–134（134 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain P 6–133（128 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain P 1–134（134 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain P 6–134（129 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL22_DEIRA
Isoform —
PDB entities 18
Chains and sequence ranges Author chain P； PDBConstruct 1–134； UniProt 1–134

50S ribosomal protein L23

OrganismNot specified

UniProt Q9RXK0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain Q； UniProt 1–95 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain R 1–94（94 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain R 2–95（94 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain R 2–95（94 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain R 1–95（95 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain R 1–94（94 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2AAR Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome. Deposited 2005-07-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain R 1–95（95 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 3.50 Å R-free 0.320
2D3O Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans Deposited 2005-09-30 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain R 0–94（95 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 3.35 Å R-free 0.322
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–95（95 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–95（95 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–95（95 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Q 1–95（95 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–95（95 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–95（95 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–95（95 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–95（95 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 1–95（95 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 1–95（95 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 1–95（95 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 2–94（93 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Q 2–94（93 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain Q 1–95（95 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 1–95（95 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 2–94（93 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 2–94（93 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Q 2–94（93 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL23_DEIRA
Isoform —
PDB entities 19
Chains and sequence ranges Author chain Q； PDBConstruct 1–95； UniProt 1–95

50S ribosomal protein L24

OrganismNot specified

UniProt Q9RXJ1

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain R； UniProt 1–115 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain S 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain S 1–115（115 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain S 1–115（115 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain S 1–115（115 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain S 1–115（115 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2D3O Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans Deposited 2005-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain S 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 3.35 Å R-free 0.322
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain R 1–115（115 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain R 1–115（115 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain R 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 1–115（115 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 1–115（115 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 2–115（114 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 1–115（115 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 4–113（110 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain R 4–113（110 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain R 1–115（115 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 1–115（115 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 4–113（110 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 4–113（110 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain R 4–113（110 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL24_DEIRA
Isoform —
PDB entities 20
Chains and sequence ranges Author chain R； PDBConstruct 1–115； UniProt 1–115

50S ribosomal protein L25

OrganismNot specified

UniProt Q9RX88

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain S； UniProt 1–237 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NJM The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) and the antibiotic sparsomycin Deposited 2003-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain T 17–253（237 aa）
Not recorded SPS SPARSOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM
Resolution 3.60 Å R-free 0.308
1NJP The crystal structure of the 50S Large ribosomal subunit from Deinococcus radiodurans complexed with a tRNA acceptor stem mimic (ASM) Deposited 2003-01-02 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: tetrameric
Chain T 17–253（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, SPARSOMYCIN; SOAKING CRYSTALS IN: 0.025mM ASM , pH 7.80
Resolution 3.50 Å R-free 0.295
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain T 1–237（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain T 17–253（237 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain T 17–253（237 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain T 1–253（253 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain T 1–237（237 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain S 1–237（237 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain S 1–237（237 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain S 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–237（237 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–237（237 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 1–237（237 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain S 1–175（175 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain S 1–237（237 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 1–237（237 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 1–175（175 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 1–175（175 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain S 1–175（175 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL25_DEIRA
Isoform —
PDB entities 21
Chains and sequence ranges Author chain S； PDBConstruct 1–237； UniProt 1–237

50S ribosomal protein L27

OrganismNot specified

UniProt Q9RY65

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain T； UniProt 1–91 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain U 1–91（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain U 1–91（91 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain U 1–91（91 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain U 1–91（91 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain U 1–91（91 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
1Y69 RRF domain I in complex with the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2004-12-04 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: pentameric
Chain U 1–91（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Resolution 3.33 Å R-free 0.338
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain T 1–91（91 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain T 1–91（91 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain T 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 1–91（91 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 1–91（91 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain T 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain T 1–91（91 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 2–85（84 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain T 2–85（84 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain T 1–91（91 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain T 1–91（91 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain T 12–85（74 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain T 1–91（91 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain T 12–83（72 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

24 other PDB entries and 24 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL27_DEIRA
Isoform —
PDB entities 22
Chains and sequence ranges Author chain T； PDBConstruct 1–91； UniProt 1–91

50S ribosomal protein L28

OrganismNot specified

UniProt Q9RRG8

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain U； UniProt 1–81 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain U 1–81（81 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain U 1–81（81 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–81（81 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain U 1–81（81 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–81（81 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–81（81 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–81（81 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–81（81 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 1–81（81 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 1–81（81 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 1–81（81 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 8–79（72 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain U 8–79（72 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain U 1–81（81 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 1–81（81 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 6–79（74 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 6–79（74 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain U 6–79（74 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

18 other PDB entries and 18 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL28_DEIRA
Isoform —
PDB entities 23
Chains and sequence ranges Author chain U； PDBConstruct 1–81； UniProt 1–81

50S ribosomal protein L29

OrganismNot specified

UniProt Q9RXJ4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain V； UniProt 1–67 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–67（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–67（67 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–67（67 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain W 1–67（67 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–67（67 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2AAR Structure of trigger factor binding domain in biologically homologous complex with eubacterial ribosome. Deposited 2005-07-14 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain W 1–67（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 20K
Resolution 3.50 Å R-free 0.320
2D3O Structure of Ribosome Binding Domain of the Trigger Factor on the 50S ribosomal subunit from D. radiodurans Deposited 2005-09-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 4 PDB declaration: pentameric
Chain W 1–67（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.8；290 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.8, VAPOR DIFFUSION, SITTING DROP, temperature 290K
Resolution 3.35 Å R-free 0.322
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain V 1–67（67 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain V 1–67（67 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain V 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–67（67 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–67（67 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain V 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain V 1–67（67 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain V 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain V 1–67（67 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain V 1–67（67 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain V 6–66（61 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain V 6–66（61 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain V 13–66（54 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

25 other PDB entries and 25 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL29_DEIRA
Isoform —
PDB entities 24
Chains and sequence ranges Author chain V； PDBConstruct 1–67； UniProt 1–67

50S ribosomal protein L30

OrganismNot specified

UniProt Q9RSL0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain W； UniProt 1–55 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain X 1–55（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain X 1–55（55 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain X 1–55（55 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain X 1–55（55 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain X 1–55（55 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–55（55 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–55（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain W 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain W 1–55（55 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain W 1–55（55 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain W 1–55（55 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain W 1–55（55 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain W 1–55（55 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL30_DEIRA
Isoform —
PDB entities 25
Chains and sequence ranges Author chain W； PDBConstruct 1–55； UniProt 1–55

50S ribosomal protein L32

OrganismNot specified

UniProt P49228

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain Y； UniProt 1–60 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1J5A STRUCTURAL BASIS FOR THE INTERACTION OF ANTIBIOTICS WITH THE PEPTIDYL TRANSFERASE CENTER IN EUBACTERIA Deposited 2002-03-06 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain M 1–60（60 aa）
Not recorded CTY CLARITHROMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.323
1JZX Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain M 1–60（60 aa）
Not recorded CLY CLINDAMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol,MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.10 Å R-free 0.303
1JZY Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain M 1–60（60 aa）
Not recorded ERY ERYTHROMYCIN A × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.301
1JZZ Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain M 1–60（60 aa）
Not recorded ROX ROXITHROMYCIN × 1 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.80 Å R-free 0.274
1K01 Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria Deposited 2001-09-17 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 3 PDB declaration: tetrameric
Chain M 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 3 CLM CHLORAMPHENICOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ethanol, dimethylhexanediol, MgCl2, KCl, Hepes, NH4Cl, pH 7.8, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.50 Å R-free 0.321
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Z 1–59（59 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Z 2–60（59 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Z 2–60（59 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1OND THE CRYSTAL STRUCTURE OF THE 50S LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS COMPLEXED WITH TROLEANDOMYCIN MACROLIDE ANTIBIOTIC Deposited 2003-02-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 2 PDB declaration: trimeric
Chain Z 1–60（60 aa）
Not recorded TAO TROLEANDOMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions EVAPORATION；EVAPORATION
Resolution 3.40 Å R-free 0.310
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain Z 1–60（60 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Z 1–59（59 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Y 1–60（60 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Z 1–60（60 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain Y 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 1–60（60 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 1–60（60 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Z 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Z 1–60（60 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 3–59（57 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Z 3–59（57 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain Z 1–60（60 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Z 1–60（60 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Z 2–59（58 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Z 2–59（58 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain Z 3–59（57 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

29 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL32_DEIRA
Isoform —
PDB entities 26
Chains and sequence ranges Author chain Y； PDBConstruct 1–60； UniProt 1–60

50S ribosomal protein L33

OrganismNot specified

UniProt Q9RSS4

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 1； UniProt 1–55 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–55（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–55（55 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–55（55 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 1 1–82（82 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–55（55 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–55（55 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–55（55 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 1 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–55（55 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–55（55 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 1 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 1 1–55（55 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 1 2–50（49 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain 1 1–55（55 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 1 2–55（54 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 1 6–54（49 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 1 6–54（49 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 1 6–54（49 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

22 other PDB entries and 22 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL33_DEIRA
Isoform —
PDB entities 27
Chains and sequence ranges Author chain 1； PDBConstruct 1–55； UniProt 1–55

50S ribosomal protein L34

OrganismNot specified

UniProt Q9RSH2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 2； UniProt 1–47 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L35 × 1 （Q9RSW6） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–47（47 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–47（47 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–47（47 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 2 1–47（47 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–47（47 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–47（47 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–47（47 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 2 1–47（47 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain 2 1–47（47 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 2 1–47（47 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 2 1–47（47 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 2 1–47（47 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 2 1–46（46 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL34_DEIRA
Isoform —
PDB entities 28
Chains and sequence ranges Author chain 2； PDBConstruct 1–47； UniProt 1–47

50S ribosomal protein L35

OrganismNot specified

UniProt Q9RSW6

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 3； UniProt 1–66 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L36 × 1 （Q9RSK0） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 1–63（63 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 2–66（65 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 2–66（65 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 3 1–66（66 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 1–65（65 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 1–66（66 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 1–66（66 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 3 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–66（66 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–66（66 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239
4U67 Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 Deposited 2014-07-28 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 3 1–66（66 aa）
Not recorded MG MAGNESIUM ION × 51 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.65 Å R-free 0.270
4WFN Crystal structure of the large ribosomal subunit (50S) of Deinococcus radiodurans containing a three residue insertion in L22 in complex with erythromycin Deposited 2014-09-16 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 3 1–65（65 aa）
Not recorded MG MAGNESIUM ION × 70 ERY ERYTHROMYCIN A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesuim chloride, Hepes, ammonium chloride, ethanol, 2-ethyl-1,3-hexadiol
Resolution 3.54 Å R-free 0.282
5DM6 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 2–66（65 aa）
Not recorded MG MAGNESIUM ION × 198 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1, 3-hexanediol, ethanol
Resolution 2.90 Å R-free 0.270
5DM7 Crystal structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with hygromycin A Deposited 2015-09-08 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 3 2–66（65 aa）
Not recorded MG MAGNESIUM ION × 186 HGR Hygromycin A × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；292 K；HEPES, sodium hydroxide, magnesium chloride, ammonium chloride, 2-mercaptoethanol, spermidine, 2-ethyl-1,3-hexanediol, ethanol
Resolution 3.00 Å R-free 0.326
5JVG The large ribosomal subunit from Deinococcus radiodurans in complex with avilamycin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 27 PDB declaration: 29-meric
Chain 3 1–66（66 aa）
Not recorded 6NO Avilamycin × 1 MG MAGNESIUM ION × 446 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 SPD SPERMIDINE × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.43 Å R-free 0.253
5JVH The crystal structure large ribosomal subunit (50S) of Deinococcus radiodurans in complex with evernimicin Deposited 2016-05-11 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 3 1–66（66 aa）
Not recorded 6O1 Evernimicin × 1 MG MAGNESIUM ION × 123 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293 K；Magnesium chloride, HEPES, ammonium chloride, ethanol, 2-ethyl-1,3-hexandiol
Resolution 3.58 Å R-free 0.247
7A0R 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 3 2–64（63 aa）
Not recorded QTZ mycinamicin II × 1 MG MAGNESIUM ION × 345 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.30 Å R-free 0.249
7A0S 50S Deinococcus radiodurans ribosome bounded with mycinamicin I Deposited 2020-08-10 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 3 2–64（63 aa）
Not recorded QU2 mycinamicin I × 1 MG MAGNESIUM ION × 367 SPD SPERMIDINE × 8 MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 4 NA SODIUM ION × 1 EOH ETHANOL × 1 CA CALCIUM ION × 5 K POTASSIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.22 Å R-free 0.253
7A18 50S Deinococcus radiodurans ribosome bounded with mycinamicin IV Deposited 2020-08-12 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 26 PDB declaration: 28-meric
Chain 3 2–64（63 aa）
Not recorded MIV MYCINAMICIN IV × 1 MG MAGNESIUM ION × 277 SPD SPERMIDINE × 7 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；293.15 K；Ribosome solution containing 0.0065 mM (180 A/ml) of D50S in 10 mM Hepes pH=7.8, 15 mM MgCl2 and 75 mM NH4Cl crystallization buffer was mixed with 10 mM spermidine, 1 % ethanol and 0.5 % 2-ethyl-1,3-hexanediol precipitants. A 0.005 ml crystallization drop was hanged over 10 % ethanol and 5% 2-ethyl-1,3-hexanediol in ddw reservoir.
Resolution 3.40 Å R-free 0.318

23 other PDB entries and 23 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL35_DEIRA
Isoform —
PDB entities 29
Chains and sequence ranges Author chain 3； PDBConstruct 1–66； UniProt 1–66

50S ribosomal protein L36

OrganismNot specified

UniProt Q9RSK0

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein–RNA Heteromer Protein × 28 RNA 2 PDB declaration: 30-meric（30） Consistent with all polymer counts Chain 4； UniProt 1–37 Not recorded rRNA-23S ribosomal RNA × 1 rRNA-5S ribosomal RNA × 1 50S ribosomal protein L2 × 1 （Q9RXJ9） 50S ribosomal protein L3 × 1 （Q9RXK2） 50S ribosomal protein L4 × 1 （Q9RXK1） 50S ribosomal protein L5 × 1 （Q9RXJ0） 50S ribosomal protein L6 × 1 （Q9RSL3） 50S ribosomal protein L11 × 1 （Q9RSS7） 50S ribosomal protein L13 × 1 （Q9RXY1） 50S ribosomal protein L14 × 1 （Q9RXJ2） 50S ribosomal protein L15 × 1 （Q9RSK9） 50S ribosomal protein L16 × 1 （Q9RXJ5） 50S ribosomal protein L17 × 1 （Q9RSJ5） 50S ribosomal protein L18 × 1 （Q9RSL2） 50S ribosomal protein L19 × 1 （Q9RWB4） 50S ribosomal protein L20 × 1 （Q9RSW7） 50S ribosomal protein L21 × 1 （Q9RY64） 50S ribosomal protein L22 × 1 （Q9RXJ7） 50S ribosomal protein L23 × 1 （Q9RXK0） 50S ribosomal protein L24 × 1 （Q9RXJ1） 50S ribosomal protein L25 × 1 （Q9RX88） 50S ribosomal protein L27 × 1 （Q9RY65） 50S ribosomal protein L28 × 1 （Q9RRG8） 50S ribosomal protein L29 × 1 （Q9RXJ4） 50S ribosomal protein L30 × 1 （Q9RSL0） 50S ribosomal protein L32 × 1 （P49228） 50S ribosomal protein L33 × 1 （Q9RSS4） 50S ribosomal protein L34 × 1 （Q9RSH2） 50S ribosomal protein L35 × 1 （Q9RSW6） MG MAGNESIUM ION × 35 ZLD N-{[(5S)-3-(3-fluoro-4-morpholin-4-ylphenyl)-2-oxo-1,3-oxazolidin-5-yl]methyl}acetamide × 1 ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；10mM MgCl2, 60mM NH4Cl, 5mM KCl, 10mM HEPES, pH7.8, VAPOR DIFFUSION, HANGING DROP Resolution 3.50 Å R-free 0.280

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB Difference from Current Entry 3DLL Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1NKW Crystal Structure Of The Large Ribosomal Subunit From Deinococcus Radiodurans Deposited 2003-01-05 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–36（36 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, VAPOR DIFFUSION, SITTING DROP
Resolution 3.10 Å R-free 0.274
1NWX COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH ABT-773 Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–37（37 aa）
Not recorded 773 CETHROMYCIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；281 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 281K
Resolution 3.50 Å R-free 0.313
1NWY COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH AZITHROMYCIN Deposited 2003-02-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–37（37 aa）
Not recorded ZIT AZITHROMYCIN × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；291 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 291K
Resolution 3.30 Å R-free 0.304
1SM1 COMPLEX OF THE LARGE RIBOSOMAL SUBUNIT FROM DEINOCOCCUS RADIODURANS WITH QUINUPRISTIN AND DALFOPRISTIN Deposited 2004-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 30 PDB declaration: 32-meric
Chain 4 1–37（37 aa）
Not recorded DOL 5-(2-DIETHYLAMINO-ETHANESULFONYL)-21-HYDROXY-10-ISOPROPYL-11,19-DIMETHYL-9,26-DIOXA-3,15,28-TRIAZA-TRICYCLO[23.2.1.00,255]OCTACOSA-1(27),12,17,19,25(28)-PENTAENE-2,8,14,23-TETRAONE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions pH 7.8；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2, KCL, HEPES, NH4CL , PH 7.80, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 290K
Resolution 3.42 Å R-free 0.348
1XBP Inhibition of peptide bond formation by pleuromutilins: The structure of the 50S ribosomal subunit from Deinococcus radiodurans in complex with Tiamulin Deposited 2004-08-31 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–37（37 aa）
Not recorded MUL TIAMULIN × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；280 K；ETHANOL, DIMETHYLHEXANEDIOL, MGCL2,KCL, HEPES, NH4CL, pH 7.80, VAPOR DIFFUSION, HANGING DROP, temperature 280K
Resolution 3.50 Å R-free 0.360
2ZJP Thiopeptide antibiotic Nosiheptide bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-07 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–37（37 aa）
Not recorded ZN ZINC ION × 2 NO1 4-(hydroxymethyl)-3-methyl-1H-indole-2-carboxylic acid × 1 MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.70 Å R-free 0.340
2ZJQ Interaction of L7 with L11 induced by Microccocin binding to the Deinococcus radiodurans 50S subunit Deposited 2008-03-08 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–37（37 aa）
Not recorded No recorded non-water small molecule X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.339
2ZJR Refined native structure of the large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2008-03-08 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–37（37 aa）
Not recorded MG MAGNESIUM ION × 35 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 2.91 Å R-free 0.311
3CF5 Thiopeptide antibiotic Thiostrepton bound to the large ribosomal subunit of Deinococcus radiodurans Deposited 2008-03-02 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 29 PDB declaration: 31-meric
Chain 4 1–37（37 aa）
Not recorded MG MAGNESIUM ION × 36 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP
Resolution 3.30 Å R-free 0.318
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–37（37 aa）
Not recorded LMA Lankamycin × 1 MG MAGNESIUM ION × 154 NA SODIUM ION × 42 K POTASSIUM ION × 15 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.25 Å R-free 0.294
3PIP Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–37（37 aa）
Not recorded LC2 N-[(1S,2R,3E,5E,7S,9E,11E,13S,15R,19R)-7,13-dihydroxy-1,4,10,19-tetramethyl-17,18-dioxo-16-oxabicyclo[13.2.2]nonadeca-3,5,9,11-tetraen-2-yl]-2-oxopropanamide × 1 LMA Lankamycin × 1 MG MAGNESIUM ION × 73 K POTASSIUM ION × 4 NA SODIUM ION × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP. 15% 2:1 ethanol:methylpentanediol was diffused to a hanging drop of 180 AU/ml solution of D50S.
Resolution 3.45 Å R-free 0.301
4IO9 Crystal structure of compound 4d bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–37（37 aa）
Not recorded MG MAGNESIUM ION × 35 1F2 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.235
4IOA Crystal structure of compound 4e bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–37（37 aa）
Not recorded MG MAGNESIUM ION × 35 1F3 (3aS,4R,7R,8S,9S,10R,11R,13R,15R,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-2-[4-(acetylamino)phenyl]-2,3-dihydro-1H-pyrrole-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.20 Å R-free 0.230
4IOC Crystal structure of compound 4f bound to large ribosomal subunit (50S) from Deinococcus radiodurans Deposited 2013-01-07 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain 4 1–37（37 aa）
Not recorded MG MAGNESIUM ION × 35 1F4 (3aS,4R,7R,8S,9S,10R,11R,13R,15S,15aR)-4-ethyl-11-methoxy-3a,7,9,11,13,15-hexamethyl-2,6,14-trioxo-10-{[3,4,6-trideoxy-3-(dimethylamino)-beta-D-xylo-hexopyranosyl]oxy}tetradecahydro-2H-oxacyclotetradecino[4,3-d][1,3]oxazol-8-yl (2R)-4,4-dimethyl-2-(pyridin-3-yl)pyrrolidine-1-carboxylate × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；VAPOR DIFFUSION, HANGING DROP
Resolution 3.60 Å R-free 0.239

14 other PDB entries and 14 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name RL36_DEIRA
Isoform —
PDB entities 30
Chains and sequence ranges Author chain 4； PDBConstruct 1–37； UniProt 1–37

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

SAXS profile for 3dll

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dll
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3dll
Deposition date deposition_date2008-06-27
Structure title titleThe oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning
Keywords keywords;Ribosome, Antibiotic, oxazolidinone, Linezolid, Ribonucleoprotein, Ribosomal protein, RNA-binding, rRNA-binding, tRNA-binding, Methylation, Metal-binding, Zinc-finger ;; RIBOSOME
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier67.98 Å
Radius of gyration Rg (electron density) rg_electron68.85 Å
Forward intensity I(0) i053588300000.00
Molecular weight molecular_weight1262600.0 kDa
Excluded volume excluded_volume1287100 ų
Envelope volume envelope_volume2142200 ų
Hydration-shell volume shell_volume237930 ų
Envelope diameter envelope_diameter230.0 Å
Shell Rg shell_rg81.20 Å
Envelope Rg envelope_rg68.53 Å
Shape Rg shape_rg69.01 Å
Total Rg total_rg68.64 Å
Total atoms total_atoms83495
Residues n_residues5812
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax229.8 Å
Rg (real space) rg_real67.79 Å
Rg uncertainty (real space) rg_real_error2.00 Å
I(0) (real space) i0_real5.3590e+10
I(0) uncertainty (real space) i0_real_error1.2440e+09
Rg (reciprocal space) rg_reciprocal68.56 Å
I(0) (reciprocal space) i0_reciprocal53660000000.0000
Solution quality estimate total_estimate0.8567
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary89.9 Å
Skewness Skewness skewness0.223
Kurtosis Kurtosis kurtosis-0.380
Angular range angular_range— – 0.1150 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9269000000.0000
Real-space data points n_real_points24
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.788; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.799
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (33)

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7. Fold Classification (SCOP + CATH) 43 domains

SCOP 2.08 (27 domains)

Domain ID domain_idd3dll11
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.8 — Zn-binding ribosomal proteins
Family Family familyg.41.8.6 — Ribosomal protein L33p
Domain ID domain_idd3dll21
Class classj — Peptides
Fold Fold foldj.118 — Ribosomal protein L34p
Superfamily Superfamily superfamilyj.118.1 — Ribosomal protein L34p
Family Family familyj.118.1.1 — Ribosomal protein L34p
Domain ID domain_idd3dll31
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.301 — L35p-like
Superfamily Superfamily superfamilyd.301.1 — L35p-like
Family Family familyd.301.1.1 — Ribosomal protein L35p
Domain ID domain_idd3dll41
Class classg — Small proteins
Fold Fold foldg.42 — Ribosomal protein L36
Superfamily Superfamily superfamilyg.42.1 — Ribosomal protein L36
Family Family familyg.42.1.1 — Ribosomal protein L36
Domain ID domain_idd3dllb1
Class classb — All beta proteins
Fold Fold foldb.43 — Reductase/isomerase/elongation factor common domain
Superfamily Superfamily superfamilyb.43.3 — Translation proteins
Family Family familyb.43.3.2 — Ribosomal protein L3
Domain ID domain_idd3dllc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.22 — Ribosomal protein L4
Superfamily Superfamily superfamilyc.22.1 — Ribosomal protein L4
Family Family familyc.22.1.1 — Ribosomal protein L4
Domain ID domain_idd3dlld1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.77 — RL5-like
Superfamily Superfamily superfamilyd.77.1 — RL5-like
Family Family familyd.77.1.1 — Ribosomal protein L5
Domain ID domain_idd3dlle1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.141 — Ribosomal protein L6
Superfamily Superfamily superfamilyd.141.1 — Ribosomal protein L6
Family Family familyd.141.1.1 — Ribosomal protein L6
Domain ID domain_idd3dlle2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.141 — Ribosomal protein L6
Superfamily Superfamily superfamilyd.141.1 — Ribosomal protein L6
Family Family familyd.141.1.1 — Ribosomal protein L6
Domain ID domain_idd3dllg1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.21 — Ribosomal protein L13
Superfamily Superfamily superfamilyc.21.1 — Ribosomal protein L13
Family Family familyc.21.1.1 — Ribosomal protein L13
Domain ID domain_idd3dllh1
Class classb — All beta proteins
Fold Fold foldb.39 — Ribosomal protein L14
Superfamily Superfamily superfamilyb.39.1 — Ribosomal protein L14
Family Family familyb.39.1.1 — Ribosomal protein L14
Domain ID domain_idd3dlli1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.12 — Ribosomal proteins L15p and L18e
Superfamily Superfamily superfamilyc.12.1 — Ribosomal proteins L15p and L18e
Family Family familyc.12.1.1 — Ribosomal proteins L15p and L18e
Domain ID domain_idd3dllj1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.41 — alpha/beta-Hammerhead
Superfamily Superfamily superfamilyd.41.4 — Ribosomal protein L16p/L10e
Family Family familyd.41.4.2 — Ribosomal protein L16p
Domain ID domain_idd3dllk1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.188 — Prokaryotic ribosomal protein L17
Superfamily Superfamily superfamilyd.188.1 — Prokaryotic ribosomal protein L17
Family Family familyd.188.1.1 — Prokaryotic ribosomal protein L17
Domain ID domain_idd3dlll1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.4 — Translational machinery components
Family Family familyc.55.4.1 — Ribosomal protein L18 and S11
Domain ID domain_idd3dllm1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.5 — Translation proteins SH3-like domain
Family Family familyb.34.5.6 — Ribosomal protein L19
Domain ID domain_idd3dlln1
Class classa — All alpha proteins
Fold Fold folda.144 — PABP domain-like
Superfamily Superfamily superfamilya.144.2 — Ribosomal protein L20
Family Family familya.144.2.1 — Ribosomal protein L20
Domain ID domain_idd3dllo1
Class classb — All beta proteins
Fold Fold foldb.155 — L21p-like
Superfamily Superfamily superfamilyb.155.1 — L21p-like
Family Family familyb.155.1.1 — Ribosomal protein L21p
Domain ID domain_idd3dllp1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.55 — Ribosomal protein L22
Superfamily Superfamily superfamilyd.55.1 — Ribosomal protein L22
Family Family familyd.55.1.1 — Ribosomal protein L22
Domain ID domain_idd3dllq1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.12 — Ribosomal proteins S24e, L23 and L15e
Superfamily Superfamily superfamilyd.12.1 — Ribosomal proteins S24e, L23 and L15e
Family Family familyd.12.1.1 — L23p
Domain ID domain_idd3dllr1
Class classb — All beta proteins
Fold Fold foldb.34 — SH3-like barrel
Superfamily Superfamily superfamilyb.34.5 — Translation proteins SH3-like domain
Family Family familyb.34.5.1 — Ribosomal proteins L24p and L21e
Domain ID domain_idd3dlls1
Class classb — All beta proteins
Fold Fold foldb.53 — Ribosomal protein L25-like
Superfamily Superfamily superfamilyb.53.1 — Ribosomal protein L25-like
Family Family familyb.53.1.1 — Ribosomal protein L25-like
Domain ID domain_idd3dllt1
Class classb — All beta proteins
Fold Fold foldb.84 — Barrel-sandwich hybrid
Superfamily Superfamily superfamilyb.84.4 — Ribosomal L27 protein-like
Family Family familyb.84.4.1 — Ribosomal L27 protein
Domain ID domain_idd3dllu1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.325 — L28p-like
Superfamily Superfamily superfamilyd.325.1 — L28p-like
Family Family familyd.325.1.1 — Ribosomal protein L28
Domain ID domain_idd3dllv1
Class classa — All alpha proteins
Fold Fold folda.2 — Long alpha-hairpin
Superfamily Superfamily superfamilya.2.2 — Ribosomal protein L29 (L29p)
Family Family familya.2.2.1 — Ribosomal protein L29 (L29p)
Domain ID domain_idd3dllw1
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.59 — Ribosomal protein L30p/L7e
Superfamily Superfamily superfamilyd.59.1 — Ribosomal protein L30p/L7e
Family Family familyd.59.1.1 — Ribosomal protein L30p/L7e
Domain ID domain_idd3dlly1
Class classg — Small proteins
Fold Fold foldg.41 — Rubredoxin-like
Superfamily Superfamily superfamilyg.41.8 — Zn-binding ribosomal proteins
Family Family familyg.41.8.5 — Ribosomal protein L32p

CATH v4.4 (16 domains)

Domain ID domain_id3dllA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology50 — OB fold (Dihydrolipoamide Acetyltransferase, E2P)
Homologous superfamily homologous superfamily140 — Nucleic acid-binding proteins
Domain ID domain_id3dllA02
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology30 — SH3 type barrels.
Homologous superfamily homologous superfamily30 —
Domain ID domain_id3dllD00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1440 — 50s Ribosomal Protein L5; Chain: A,
Homologous superfamily homologous superfamily10 — Ribosomal protein L5
Domain ID domain_id3dllE01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily12 — Ribosomal protein L6
Domain ID domain_id3dllE02
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology930 — Outer Surface Protein A; domain 3
Homologous superfamily homologous superfamily12 — Ribosomal protein L6
Domain ID domain_id3dllF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology10 — Arc Repressor Mutant, subunit A
Homologous superfamily homologous superfamily250 — Ribosomal protein L11/L12, C-terminal domain
Domain ID domain_id3dllG00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1180 — Ribosomal Protein L13p; Chain: A;
Homologous superfamily homologous superfamily10 — Ribosomal protein L13
Domain ID domain_id3dllH00
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology150 — Ribosomal Protein L14
Homologous superfamily homologous superfamily20 — Ribosomal protein L14/L23
Domain ID domain_id3dllJ01
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1170 — Aldehyde Oxidoreductase; domain 3
Homologous superfamily homologous superfamily10 — Ribosomal protein L16/L10
Domain ID domain_id3dllK00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1030 — 50s Ribosomal Protein L17; Chain: A,
Homologous superfamily homologous superfamily10 — Ribosomal protein L17
Domain ID domain_id3dllL01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily100 —
Domain ID domain_id3dllP00
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology470 — Ribosomal Protein L22; Chain A
Homologous superfamily homologous superfamily10 — Ribosomal protein L22/L17
Domain ID domain_id3dllQ00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily330 — RRM (RNA recognition motif) domain
Domain ID domain_id3dllS01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology240 — Ribosomal Protein L25; Chain P
Homologous superfamily homologous superfamily10 — Ribosomal Protein L25; Chain P
Domain ID domain_id3dllS02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology120 — RNA Polymerase Alpha Subunit; Chain A, domain 2
Homologous superfamily homologous superfamily20 — Ribosomal protein L25, C-terminal domain
Domain ID domain_id3dllW00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1390 — Ribosomal Protein L30; Chain: A,
Homologous superfamily homologous superfamily20 — Ribosomal protein L30/L7
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8. Citations (1)

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9. Files and Curves (10)