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4twa

Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum

Method: X-RAY DIFFRACTION Dmax: 102.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proline--tRNA ligase

Plasmodium falciparum

UniProt Q8I5R7

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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 254–746 Chain B； UniProt 254–746 Fragment：UNP residues 254-746 CL CHLORIDE ION × 6 SO4 SULFATE ION × 11 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.8 M lithium sulphate monohydrate and 0.1 M sodium acetate Resolution 3.00 Å R-free 0.249
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 254–746 Chain B； UniProt 254–746 Fragment：UNP residues 254-746 CL CHLORIDE ION × 12 SO4 SULFATE ION × 22 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；0.8 M lithium sulphate monohydrate and 0.1 M sodium acetate Resolution 3.00 Å R-free 0.249

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 4TWA Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
4NCX Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum 3D7 Deposited 2013-10-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–746（498 aa） Fragment：C-terimus residues 249-746
Chain B 249–746（498 aa） Fragment：C-terimus residues 249-746
Not recorded EDO 1,2-ETHANEDIOL × 6 CL CHLORIDE ION × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；Morpheus(b2): 0.1M each MES, Imidazole, pH 6.5, 0.09M each NaF, NaBr, NaI, 30% ethylene glycol, PEG-8000 and 5mM L-Proline, 5mM ATP, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 1.85 Å R-free 0.206
4OLF Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase)from Plasmodium falciparum in complex with Halofuginone and AMPPNP Deposited 2014-01-23 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 1 SO4 SULFATE ION × 15 NA SODIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for 5min, then added 1 to 1 with Wiz3/4(h5)- 20%PEG-8000, 0.1M HEPES/NaOH, pH=7.5, 10% isopropanol, 0.2M AmSO4, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.90 Å R-free 0.236
4OLF Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase)from Plasmodium falciparum in complex with Halofuginone and AMPPNP Deposited 2014-01-23 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 2 SO4 SULFATE ION × 30 NA SODIUM ION × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for 5min, then added 1 to 1 with Wiz3/4(h5)- 20%PEG-8000, 0.1M HEPES/NaOH, pH=7.5, 10% isopropanol, 0.2M AmSO4, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.90 Å R-free 0.236
4Q15 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Halofuginone and AMPPNP in space group P212121 at 2.35 A Deposited 2014-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.35 Å R-free 0.219
4Q15 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Halofuginone and AMPPNP in space group P212121 at 2.35 A Deposited 2014-04-02 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.35 Å R-free 0.219
4Q15 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Halofuginone and AMPPNP in space group P212121 at 2.35 A Deposited 2014-04-02 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Chain B 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded MG MAGNESIUM ION × 2 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 2 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；289 K；Protein incubated with 4mM each of AMPPnP, halofuginone, B-ME, and MgCl2 for ~5min, then added 1 to 1 with Wiz1/2(a10): 20% PEG-2000 MME, 0.1M Tris base/HCl, pH=7.0, cryoprotected with 20%EG, VAPOR DIFFUSION, SITTING DROP, temperature 289K
Resolution 2.35 Å R-free 0.219
4WI1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506 Deposited 2014-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded 3O6 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea × 1 EDO 1,2-ETHANEDIOL × 7 MG MAGNESIUM ION × 1 IMD IMIDAZOLE × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride
Resolution 1.65 Å R-free 0.188
4WI1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506 Deposited 2014-09-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded 3O6 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea × 1 EDO 1,2-ETHANEDIOL × 7 IMD IMIDAZOLE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride
Resolution 1.65 Å R-free 0.188
4WI1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506 Deposited 2014-09-25 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Chain B 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded 3O6 1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea × 4 EDO 1,2-ETHANEDIOL × 28 MG MAGNESIUM ION × 2 IMD IMIDAZOLE × 4 CL CHLORIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 21.9mg/ml, incubated with 5mM TCMDC-124506, then 1:1 with Morpheus(B2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each magnesium chloride, calcium chloride
Resolution 1.65 Å R-free 0.188
4YDQ Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum in complex with Halofuginone and AMPPNP Deposited 2015-02-23 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 254–746（493 aa） Fragment：UNP residues 254-746
Chain B 254–746（493 aa） Fragment：UNP residues 254-746
Not recorded ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 2 HFG 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one × 2 MG MAGNESIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M Bis-Tris pH 6.5, 2 % (v/v) Tacsimate pH 5.0 and 12 % (w/v) Polyethylene glycol 3,350.
Resolution 2.30 Å R-free 0.232
5IFU Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide Deposited 2016-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded GBM 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 1 CL CHLORIDE ION × 1 FMT FORMIC ACID × 10 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate
Resolution 2.45 Å R-free 0.213
5IFU Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide Deposited 2016-02-26 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain B 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded GBM 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 1 FMT FORMIC ACID × 4 EDO 1,2-ETHANEDIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate
Resolution 2.45 Å R-free 0.213
5IFU Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with Glyburide Deposited 2016-02-26 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Chain B 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded GBM 5-chloro-N-(2-{4-[(cyclohexylcarbamoyl)sulfamoyl]phenyl}ethyl)-2-methoxybenzamide × 4 CL CHLORIDE ION × 2 FMT FORMIC ACID × 28 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；289 K；at 22mg/ml, incubated with 5mM glyburide, then 1:1 with Morpheus(g2): 10% PEG-8000, 20% ethylene glycol, 0.1M MES/imidazole, pH=6.5, 0.03M each sodium formate, ammonium acetate, trisodium citrate, sodium potassium tartrate, sodium oxamate
Resolution 2.45 Å R-free 0.213
6T7K Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with NCP-26 and L-Proline Deposited 2019-10-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa）
Not recorded PRO PROLINE × 1 MU5 ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-(piperidin-1-ylcarbonylamino)pyrazine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 21 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.1 M Hepes pH 7.5 20% PEG 1000, 2 mM Pro
Resolution 1.79 Å R-free 0.194
7F96 Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L95 Deposited 2021-07-04 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 254–746（493 aa） Fragment：UNP residues 254-746
Not recorded JE6 ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide × 2 PRO PROLINE × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；0.2 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base); BICINE) and 30 % v/v Precipitant Mix (40% v/v Ethylene glycol; 20% w/v PEG 8000)
Resolution 2.58 Å R-free 0.191
7F97 Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97 Deposited 2021-07-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 254–746（493 aa） Fragment：UNP residues 254-746
Chain B 254–746（493 aa） Fragment：UNP residues 254-746
Not recorded PRO PROLINE × 2 1XK 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide × 2 BU1 1,4-BUTANEDIOL × 1 CL CHLORIDE ION × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base), BICINE), 37.5 % v/v Precipitant (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)
Resolution 2.39 Å R-free 0.232
7F97 Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with L-proline and compound L97 Deposited 2021-07-04 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain C 254–746（493 aa） Fragment：UNP residues 254-746
Chain D 254–746（493 aa） Fragment：UNP residues 254-746
Not recorded PRO PROLINE × 2 1XK 4-[(3S)-3-cyclopropyl-3-(hydroxymethyl)-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(1-methylpyrazol-4-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide × 2 CL CHLORIDE ION × 4 HEZ HEXANE-1,6-DIOL × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.12 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Tris (base), BICINE), 37.5 % v/v Precipitant (25% v/v MPD, 25% PEG 1000, 25% w/v PEG 3350)
Resolution 2.39 Å R-free 0.232
7QB7 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT345 and L-Proline Deposited 2021-11-18 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa）
Not recorded PRO PROLINE × 1 EDO 1,2-ETHANEDIOL × 13 9X2 ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[[(2~{S})-pyrrolidin-2-yl]carbonylamino]methyl]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；293.15 K；25% PEG3350, 0.1M Bis-Tris
Resolution 1.90 Å R-free 0.210
7QC1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436 Deposited 2021-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa）
Not recorded 9XM [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate × 1 EDO 1,2-ETHANEDIOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5 M Malic acid
Resolution 2.51 Å R-free 0.233
7QC1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436 Deposited 2021-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain D 249–746（498 aa）
Not recorded 9XM [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate × 1 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5 M Malic acid
Resolution 2.51 Å R-free 0.233
7QC1 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT436 Deposited 2021-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain I 249–746（498 aa）
Not recorded 9XM [(2~{R},3~{S})-2-[3-(7-bromanyl-6-chloranyl-4-oxidanylidene-quinazolin-3-yl)-2-oxidanylidene-propyl]piperidin-3-yl] ~{N}-[4-[[3-(2,3-dihydro-1~{H}-inden-2-ylcarbamoyl)pyrazin-2-yl]carbamoyl]piperazin-1-yl]sulfonylcarbamate × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；1.5 M Malic acid
Resolution 2.51 Å R-free 0.233
7QC2 Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline-tRNA ligase) from Plasmodium falciparum in complex with MAT334 and L-Proline Deposited 2021-11-22 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric
Chain A 249–746（498 aa）
Not recorded PRO PROLINE × 1 AJT ~{N}-(2,3-dihydro-1~{H}-inden-2-yl)-3-[[4-[[(2~{S})-pyrrolidin-2-yl]carbonylamino]piperidin-1-yl]carbonylamino]pyrazine-2-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；293.15 K；0.2 M L-Pro, 10 % PEG3350, 0.1 M Hepes
Resolution 2.28 Å R-free 0.253
7V9D Plasmodium falciparum Prolyl-tRNA Synthetase (PfPRS) in Complex with inhibitor L95 and azetidine Deposited 2021-08-24 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 254–746（493 aa）
Not recorded JE6 ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide × 2 02A (2S)-azetidine-2-carboxylic acid × 2 EDO 1,2-ETHANEDIOL × 6 ACT ACETATE ION × 2 BU1 1,4-BUTANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.12 M Alcohols (0.2M 1,6-Hexanediol, 0.2M 1-Butanol, 0.2M 1,2-Propanediol, 0.2M 2-Propanol, 0.2M 1,4-Butanediol, 0.2M 1,3-Propanediol), 0.1 M Buffer (Imidazole, MES monohydrate), 30 % v/v Precipitant (40% v/v Ethylene glycol, 20% w/v PEG 8000)
Resolution 1.94 Å R-free 0.200
9YON Crystal structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with inhibitor YNW69 Deposited 2025-10-13 Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 249–746（498 aa） Fragment：UNP residues 249-746
Not recorded CL CHLORIDE ION × 10 SO4 SULFATE ION × 10 A1CYM N-[(3M)-3-(4-aminothieno[3,2-d]pyrimidin-6-yl)benzene-1-sulfonyl]-L-prolinamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 5；291 K；Grid Salt screen H8 : 4.0M NaCl, 0.1M Citric acid/citrate, pH 5.0. CrpaA.01302.a.B2.PW39348 at 21.9 mg/mL. 2mM inhibitor added to the protein prior to crystallization. plate 19968 H8 drop 1, Puck: PSL-1107, Cryo: 2.5M Lithium sulfate. The data were somewhat anisotropic which produced residual density (Fo-Fc) thoughout the polypeptide. The anisotropically truncated data from staraniso were used for refinement. The original and anisotropic truncated data were both deposited.
Resolution 2.43 Å R-free 0.233

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

View Construct and Data Evidence
UniProt name SYP_PLAF7
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 5–497； UniProt 254–746 Author chain B； PDBConstruct 5–497； UniProt 254–746

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 4twa

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4twa
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4twa
Deposition date deposition_date2014-06-30
Structure title titleCrystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum
Keywords keywordsProtein translation, Halofuginone, Malaria, Inhibitor, PRS, Synthetase, LIGASE; LIGASE
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_guinier32.20 Å
Radius of gyration Rg (electron density) rg_electron31.08 Å
Forward intensity I(0) i0189222000.00
Molecular weight molecular_weight111620.0 kDa
Excluded volume excluded_volume140180 ų
Envelope volume envelope_volume172980 ų
Hydration-shell volume shell_volume45427 ų
Envelope diameter envelope_diameter109.2 Å
Shell Rg shell_rg38.92 Å
Envelope Rg envelope_rg31.17 Å
Shape Rg shape_rg31.03 Å
Total Rg total_rg31.91 Å
Total atoms total_atoms7847
Residues n_residues968
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 dmax102.8 Å
Rg (real space) rg_real32.04 Å
Rg uncertainty (real space) rg_real_error0.61 Å
I(0) (real space) i0_real1.8920e+08
I(0) uncertainty (real space) i0_real_error2.8590e+06
Rg (reciprocal space) rg_reciprocal32.11 Å
I(0) (reciprocal space) i0_reciprocal189200000.0000
Solution quality estimate total_estimate0.8993
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary39.8 Å
Skewness Skewness skewness0.190
Kurtosis Kurtosis kurtosis-0.490
Angular range angular_range— – 0.2450 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha32050000.0000
Real-space data points n_real_points50
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.915; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.996; Smooth: 0.947
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id4twaA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id4twaA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id4twaA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily30 — C-terminal domain of ProRS
Domain ID domain_id4twaB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily10 — Bira Bifunctional Protein; Domain 2
Domain ID domain_id4twaB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily800 — Anticodon-binding domain
Domain ID domain_id4twaB03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily30 — C-terminal domain of ProRS
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8. Citations (1)

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9. Files and Curves (10)