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1k01

Structural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria

Method: X-RAY DIFFRACTION Dmax: 214.5 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

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 × 3 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain K； UniProt 1–205 Not recorded 23S rRNA × 1 Ribosomal Protein L22 × 1 （Q9RXJ7） Ribosomal Protein L32 × 1 （P49228） 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

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 1K01 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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
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 oligomeric state 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
3DLL The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning Deposited 2008-06-27 Different oligomeric state 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 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
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 2
Chains and sequence ranges Author chain K； PDBConstruct 1–205； UniProt 1–205

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 × 3 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain L； UniProt 1–134 Not recorded 23S rRNA × 1 Ribosomal Protein L4 × 1 （Q9RXK1） Ribosomal Protein L32 × 1 （P49228） 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

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 1K01 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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
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 oligomeric state 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
3DLL The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning Deposited 2008-06-27 Different oligomeric state 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 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
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 3
Chains and sequence ranges Author chain L； PDBConstruct 1–134； UniProt 1–134

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 × 3 RNA 1 PDB declaration: tetrameric（4） Consistent with all polymer counts Chain M； UniProt 1–60 Not recorded 23S rRNA × 1 Ribosomal Protein L4 × 1 （Q9RXK1） Ribosomal Protein L22 × 1 （Q9RXJ7） 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

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 1K01 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 ligand/ion 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 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 ligand/ion 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 ligand/ion 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
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 oligomeric state 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
3DLL The oxazolidinone antibiotics perturb the ribosomal peptidyl-transferase center and effect tRNA positioning Deposited 2008-06-27 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein–RNA Heteromer；Protein × 28 PDB declaration: 30-meric
Chain Y 1–60（60 aa）
Not recorded 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
3PIO Crystal structure of the synergistic antibiotic pair lankamycin and lankacidin in complex with the large ribosomal subunit Deposited 2010-11-07 Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 4
Chains and sequence ranges Author chain M； PDBConstruct 1–60； UniProt 1–60

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 1k01

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1k01
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1k01
Deposition date deposition_date2001-09-17
Structure title titleStructural Basis for the Interaction of Antibiotics with the Peptidyl Transferase Center in Eubacteria
Keywords keywordsRibosome, 50S, 23S, 5S, Antibiotics, Chloramphenicol, Peptidyl transferase center; 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_guinier64.94 Å
Radius of gyration Rg (electron density) rg_electron64.50 Å
Forward intensity I(0) i037347200000.00
Molecular weight molecular_weight945110.0 kDa
Excluded volume excluded_volume892220 ų
Envelope volume envelope_volume1671500 ų
Hydration-shell volume shell_volume201720 ų
Envelope diameter envelope_diameter249.0 Å
Shell Rg shell_rg74.68 Å
Envelope Rg envelope_rg64.20 Å
Shape Rg shape_rg64.51 Å
Total Rg total_rg64.57 Å
Total atoms total_atoms59555
Residues n_residues2774
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 dmax214.5 Å
Rg (real space) rg_real64.59 Å
Rg uncertainty (real space) rg_real_error1.37 Å
I(0) (real space) i0_real3.7350e+10
I(0) uncertainty (real space) i0_real_error7.5620e+08
Rg (reciprocal space) rg_reciprocal65.22 Å
I(0) (reciprocal space) i0_reciprocal37390000000.0000
Solution quality estimate total_estimate0.8561
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary80.5 Å
Skewness Skewness skewness0.256
Kurtosis Kurtosis kurtosis-0.273
Angular range angular_range— – 0.1200 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3478000000.0000
Real-space data points n_real_points25
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.806; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.946; Smooth: 0.762
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1k01k_
Class classi — Low resolution protein structures
Fold Fold foldi.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
Family Family familyi.1.1.2 — Large subunit
Domain ID domain_idd1k01l_
Class classi — Low resolution protein structures
Fold Fold foldi.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
Family Family familyi.1.1.2 — Large subunit
Domain ID domain_idd1k01m_
Class classi — Low resolution protein structures
Fold Fold foldi.1 — Ribosome and ribosomal fragments
Superfamily Superfamily superfamilyi.1.1 — Ribosome and ribosomal fragments
Family Family familyi.1.1.2 — Large subunit
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8. Citations (1)

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9. Files and Curves (10)