SMTL ID : 7f9a.1

Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L97

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x 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(Non-covalent)

1XK.1: 20 residues within 4Å: Chain A: R.145, E.147, K.149, H.150, P.151, F.154, L.155, R.156, T.157, R.158, F.160, W.162, Q.230, G.231, G.232, T.233, G.267, T.269, R.271 Ligands: PRO.13 15 PLIP interactions: 15 interactions with chain A Hydrophobic interactions: A:E.147, A:K.149, A:R.156, A:R.158, A:F.160, A:W.162, A:T.269 Hydrogen bonds: A:R.156, A:T.157, A:T.157, A:Q.230, A:R.271 Water bridges: A:E.147 pi-Stacking: A:F.160 pi-Cation interactions: A:R.156 1XK.14: 19 residues within 4Å: Chain B: R.145, E.147, K.149, H.150, P.151, F.154, L.155, R.156, T.157, R.158, F.160, W.162, Q.230, G.231, G.232, T.233, G.267, T.269, R.271 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:E.147, B:K.149, B:R.156, B:R.158, B:F.160, B:W.162, B:T.269 Hydrogen bonds: B:R.156, B:T.157, B:T.157, B:Q.230, B:G.232 Water bridges: B:T.269 pi-Stacking: B:F.160

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.441, C.446, C.488, C.490 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.441, A:C.446, A:C.488, A:C.490 ZN.15: 4 residues within 4Å: Chain B: C.441, C.446, C.488, C.490 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.441, B:C.446, B:C.488, B:C.490

10 x CA: CALCIUM ION(Non-covalent)

CA.3: 1 residues within 4Å: Chain A: E.443 5 PLIP interactions: 2 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:E.443, A:E.443, H2O.4, H2O.4, H2O.5 CA.4: 2 residues within 4Å: Chain A: D.89, E.93 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.89, A:E.93, A:E.93, H2O.1, H2O.2 CA.5: 1 residues within 4Å: Chain A: D.89 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.89 CA.6: 2 residues within 4Å: Chain A: P.44, C.294 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.294 CA.7: 1 residues within 4Å: Chain A: E.207 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.207, H2O.5 CA.8: 2 residues within 4Å: Chain A: D.459, L.460 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.459 CA.11: 4 residues within 4Å: Chain A: E.67 Chain B: P.44, W.45, C.294 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:E.67 CA.16: 2 residues within 4Å: Chain B: D.89, E.93 5 PLIP interactions: 2 interactions with chain B, 3 Ligand-Water interactions Metal complexes: B:D.89, B:E.93, H2O.6, H2O.8, H2O.9 CA.17: 3 residues within 4Å: Chain B: E.257, K.258 Ligands: CA.18 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.257 CA.18: 2 residues within 4Å: Chain B: E.257 Ligands: CA.17 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:E.257

3 x CL: CHLORIDE ION(Non-functional Binders)

CL.9: 5 residues within 4Å: Chain A: L.9, E.10, A.11, Q.23, K.27 Ligand excluded by PLIP CL.10: 1 residues within 4Å: Chain A: H.416 Ligand excluded by PLIP CL.12: 4 residues within 4Å: Chain A: L.105, A.106 Chain B: W.146, F.148 Ligand excluded by PLIP

2 x PRO: PROLINE(Non-covalent)

PRO.13: 12 residues within 4Å: Chain A: T.114, E.116, R.145, W.162, E.164, H.166, F.209, H.235, S.265, W.266, G.267 Ligands: 1XK.1 12 PLIP interactions: 10 interactions with chain A, 2 Ligand-Ligand interactions Hydrophobic interactions: A:W.162, A:E.164 Hydrogen bonds: A:T.114, A:T.114, A:T.114, A:S.265, P.13, P.13 Water bridges: A:R.145, A:R.145 Salt bridges: A:R.145, A:H.235 PRO.19: 12 residues within 4Å: Chain B: T.114, E.116, R.145, W.162, E.164, H.166, F.209, T.233, H.235, S.265, W.266, G.267 11 PLIP interactions: 10 interactions with chain B, 1 Ligand-Ligand interactions Hydrophobic interactions: B:W.162, B:E.164 Hydrogen bonds: B:T.114, B:T.233, B:T.233, B:S.265, P.19 Water bridges: B:R.145, B:R.145 Salt bridges: B:R.145, B:H.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yogavel, M. et al., Targeting prolyl-tRNA synthetase via a series of ATP-mimetics to accelerate drug discovery against toxoplasmosis. Plos Pathog. (2023)

Release Date

2022-10-05

Peptides

Bifunctional glutamate/proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional glutamate/proline--tRNA ligase

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