SAXSdb — 4wi1

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1. Protein Identity and Related Structures Protein Identity & Related Structures

Proline--tRNA ligase

Plasmodium falciparum

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 249–746	Fragment：UNP residues 249-746	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 249–746	Fragment：UNP residues 249-746	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
3	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 249–746 Chain B； UniProt 249–746	Fragment：UNP residues 249-746	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

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 4WI1	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 oligomeric state 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 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 oligomeric state 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 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 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 oligomeric state 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
4TWA Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum Deposited 2014-06-30	Different construct Different oligomeric state 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	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
4TWA Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum Deposited 2014-06-30	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 254–746（493 aa） Fragment：UNP residues 254-746 Chain B 254–746（493 aa） Fragment：UNP residues 254-746	Not recorded	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
4YDQ Crystal Structure of Prolyl-tRNA Synthetase (PRS) from Plasmodium falciparum in complex with Halofuginone and AMPPNP Deposited 2015-02-23	Different construct Different oligomeric state 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 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 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 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 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 oligomeric state 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 construct Different oligomeric state 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 construct Different oligomeric state 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 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 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 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 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 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 oligomeric state 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 oligomeric state 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 23 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 9–506； UniProt 249–746 Author chain B； PDBConstruct 9–506； UniProt 249–746

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4wi1
Deposition date deposition_date	2014-09-25
Structure title title	Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506
Keywords keywords	;SSGCID, Plasmodium falciparum, Prolyl-tRNA synthetase, ProRS, Proline--tRNA ligase, Structural Genomics, Seattle Structural Genomics Center for Infectious Disease, LIGASE ;; LIGASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	32.29 Å
Radius of gyration Rg (electron density) rg_electron	31.26 Å
Forward intensity I(0) i0	155920000.00
Molecular weight molecular_weight	101630.0 kDa
Excluded volume excluded_volume	127840 Å³
Envelope volume envelope_volume	156660 Å³
Hydration-shell volume shell_volume	41491 Å³
Envelope diameter envelope_diameter	114.0 Å
Shell Rg shell_rg	38.50 Å
Envelope Rg envelope_rg	31.27 Å
Shape Rg shape_rg	31.21 Å
Total Rg total_rg	32.03 Å
Total atoms total_atoms	7159
Residues n_residues	875
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	105.7 Å
Rg (real space) rg_real	32.16 Å
Rg uncertainty (real space) rg_real_error	0.66 Å
I(0) (real space) i0_real	1.5590e+08
I(0) uncertainty (real space) i0_real_error	2.4480e+06
Rg (reciprocal space) rg_reciprocal	32.22 Å
I(0) (reciprocal space) i0_reciprocal	155900000.0000
Solution quality estimate total_estimate	0.8989
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	38.8 Å
Skewness Skewness skewness	0.173
Kurtosis Kurtosis kurtosis	-0.560
Angular range angular_range	— – 0.2450 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	20820000.0000
Real-space data points n_real_points	50
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.899; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.983

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Proline--tRNA ligase
Molecular weight formula_weight	58986.5 kDa
EC 编号 ec_number	6.1.1.15
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	8093

MAHHHHHHSNILGITSKKIENFSDWYTQVIVKSELIEYYDISGCYILRPAAYYIWECVQAFFNKEIKKLNVENSYFPLFVTKNKLEKEKNHIEGFSPEVAWVTKYGDSNLPEEIAIRPTSETIMYSVFPKWIRSYRDLPLKLNQWNTVVRWEFKQPTPFIRTREFLWQEGHTAHKNEEEAVKLVFDILDLYRRWYEEYLAVPIIKGIKSEGEKFGGANFTSTAEAFISENGRAIQAATSHYLGTNFAKMFKIEFEDENEVKQYVHQTSWGCTTRSIGIMIMTHGDDKGLVLPPNVSKYKVVIVPIFYKTTDENAIHSYCKDIEKILKNAQINCVYDDRASYSPGYKFNHWELRGIPIRIEVGPKDLQNNSCVIVRRDNNEKCNVKKESVLLETQQMLVDIHKNLFLKAKKKLDDSIVQVTSFSEVMNALNKKKMVLAPWCEDIATEEEIKKETQRLSLNQTNSETTLSGAMKPLCIPLDQPPMPPNMKCFWSGKPAKRWCLFGRSY

来源 Source

来源生物 organism	Plasmodium falciparum
NCBI Class编号 ncbi_taxonomy_id	36329
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	1-(4-fluorophenyl)-3-[4-(4-fluorophenyl)-1-methyl-3-(trifluoromethyl)-1H-pyrazol-5-yl]urea
Molecular weight formula_weight	396.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	14

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	IMIDAZOLE
Molecular weight formula_weight	69.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	765

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id	4wi1A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	4wi1A02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	4wi1A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

Domain ID domain_id	4wi1B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	930 — BirA Bifunctional Protein; domain 2
Homologous superfamily homologous superfamily	10 — Bira Bifunctional Protein; Domain 2

Domain ID domain_id	4wi1B02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	800 — Anticodon-binding domain

Domain ID domain_id	4wi1B03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	110 — Translation Initiation Factor IF3
Homologous superfamily homologous superfamily	30 — C-terminal domain of ProRS

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8. Citations (1)

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Unit-cell length a length_a	148.180 Å
Unit-cell length b length_b	91.340 Å
Unit-cell length c length_c	110.910 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	129.53 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.650 Å
Low-resolution limit resolution_low	40.288 Å
R factor r_factor	0.1620
R_work r_work	0.1616
R_free r_free	0.1879

fit	/app/data/saxs_computation/wi/4wi1/4wi1.fit
pddf	/app/data/pr_computation/wi/4wi1/4wi1.pr.out
profile	/app/data/saxs_computation/wi/4wi1/4wi1.dat

Crystal Structure of Prolyl-tRNA synthetase (ProRS, Proline--tRNA ligase) from Plasmodium falciparum in complex with TCMDC-124506