SMTL ID : 7f9c.1

Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with L-proline and compound L96

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.20 Å

Oligo State

homo-dimer

Ligands

2 x 1UI: 4-[(3S)-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-N-[[3-fluoranyl-5-(5-methoxypyridin-3-yl)phenyl]methyl]-6-methyl-pyridine-2-carboxamide(Non-covalent)

1UI.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.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:E.147, A:R.156, A:R.158, A:F.160, A:W.162, A:T.233, A:T.269 Hydrogen bonds: A:R.156, A:T.157, A:T.157 pi-Stacking: A:F.160 1UI.9: 20 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 Ligands: PRO.16 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:E.147, B:K.149, B:R.158, B:F.160, B:W.162, B:T.233, B:T.269 Hydrogen bonds: B:K.149, B:R.156, B:T.157, B:T.157 Water bridges: B:R.145 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.10: 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

6 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: S.369, Q.371 No protein-ligand interaction detected (PLIP) CA.6: 2 residues within 4Å: Chain A: D.89, E.93 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.89, A:E.93, H2O.1, H2O.4 CA.7: 1 residues within 4Å: Chain A: D.19 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:D.19 CA.11: 2 residues within 4Å: Chain B: D.89, E.93 4 PLIP interactions: 2 interactions with chain B, 2 Ligand-Water interactions Metal complexes: B:D.89, B:E.93, H2O.7, H2O.7 CA.12: 1 residues within 4Å: Chain B: D.213 No protein-ligand interaction detected (PLIP) CA.14: 1 residues within 4Å: Chain B: G.256 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:G.256

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

CL.4: 3 residues within 4Å: Chain A: K.200, F.476, K.477 Ligand excluded by PLIP CL.5: 3 residues within 4Å: Chain A: L.105, A.106 Chain B: W.146 Ligand excluded by PLIP CL.13: 4 residues within 4Å: Chain B: R.335, A.336, L.338, R.339 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: L.17, A.18, Q.152, M.278 Ligand excluded by PLIP

2 x PRO: PROLINE(Non-covalent)

PRO.8: 13 residues within 4Å: Chain A: T.114, E.116, R.145, W.162, E.164, H.166, F.209, T.233, H.235, S.265, W.266, G.267 Ligands: 1UI.1 11 PLIP interactions: 9 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:S.265, P.8, P.8 Water bridges: A:R.145, A:R.145 Salt bridges: A:R.145, A:H.235 PRO.16: 13 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 Ligands: 1UI.9 9 PLIP interactions: 1 Ligand-Ligand interactions, 8 interactions with chain B Hydrogen bonds: P.16, B:T.114, B:S.265 Hydrophobic interactions: B:W.162, B:E.164 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

2022-07-06

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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