SMTL ID : 7x09.1

Homo sapiens Prolyl-tRNA Synthetase (HsPRS) in Complex with inhibitors L95 and Halofuginone

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.70 Å

Oligo State

homo-dimer

Ligands

2 x HFG: 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one(Non-covalent)

HFG.1: 18 residues within 4Å: Chain A: P.92, E.93, V.94, P.113, 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: JE6.2, BR.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:P.113, A:P.113, A:W.162, A:W.162, A:E.164, A:F.209 Hydrogen bonds: A:T.114, A:T.114, A:R.145, A:S.265 Water bridges: A:R.145, A:R.145 HFG.8: 19 residues within 4Å: Chain B: H.86, F.90, E.93, V.94, P.113, 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: JE6.9, BR.11 15 PLIP interactions: 15 interactions with chain B Hydrophobic interactions: B:H.86, B:F.90, B:P.113, B:P.113, B:T.114, B:W.162, B:W.162, B:E.164, B:F.209 Hydrogen bonds: B:T.114, B:R.145, B:S.265 Water bridges: B:R.145 pi-Stacking: B:F.90, B:F.90

2 x JE6: ~{N}-[4-[(3~{S})-3-cyano-3-cyclopropyl-2-oxidanylidene-pyrrolidin-1-yl]-6-methyl-pyridin-2-yl]-2-phenyl-ethanamide(Non-covalent)

JE6.2: 20 residues within 4Å: Chain A: R.145, E.147, K.149, H.150, F.154, L.155, R.156, T.157, R.158, F.160, Q.230, G.231, G.232, T.233, G.267, L.268, T.269, R.271 Ligands: HFG.1, BR.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.145, A:E.147, A:K.149, A:R.156, A:F.160, A:T.233, A:T.269 Hydrogen bonds: A:T.157, A:T.157, A:R.271 Water bridges: A:R.145 pi-Stacking: A:F.160 JE6.9: 21 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, Q.230, G.231, G.232, T.233, G.267, L.268, T.269, R.271 Ligands: HFG.8, BR.11 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:R.145, B:E.147, B:P.151, B:F.160, B:T.233, B:T.269 Hydrogen bonds: B:T.157, B:T.157, B:T.269, B:R.271 pi-Stacking: B:F.160

4 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: C.441, C.446, C.488, C.490, N.493 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.441, A:C.446, A:C.488, A:C.490 ZN.5: 3 residues within 4Å: Chain A: A.48, C.294 Chain B: E.67 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:C.294 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 ZN.12: 3 residues within 4Å: Chain A: E.67 Chain B: P.44, C.294 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:C.294

2 x BR: BROMIDE ION(Non-covalent)

BR.4: 3 residues within 4Å: Chain A: R.145 Ligands: HFG.1, JE6.2 Ligand excluded by PLIP BR.11: 3 residues within 4Å: Chain B: R.145 Ligands: HFG.8, JE6.9 Ligand excluded by PLIP

3 x CA: CALCIUM ION(Non-covalent)

CA.6: 1 residues within 4Å: Chain A: E.257 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.257, A:E.257, H2O.10 CA.13: 1 residues within 4Å: Chain B: H.416 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:H.416, H2O.13, H2O.16, H2O.17, H2O.22 CA.16: 1 residues within 4Å: Chain B: E.257 5 PLIP interactions: 1 interactions with chain B, 4 Ligand-Water interactions Metal complexes: B:E.257, H2O.16, H2O.19, H2O.19, H2O.22

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 9 residues within 4Å: Chain A: Y.70, R.112, C.141, N.142 Chain B: Y.70, R.112, W.140, C.141, N.142 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:Y.70, A:Y.70, A:N.142, B:Y.70, B:R.112, B:N.142

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

CL.14: 3 residues within 4Å: Chain B: R.326, E.387, N.388 Ligand excluded by PLIP CL.15: 4 residues within 4Å: Chain B: P.290, R.291, Q.296, R.333 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Manickam, Y. et al., Crystal structure of Homo sapiens Prolyl-tRNA synthetase (HsPRS) with double inhibitors (HF and L95). To Be Published

Release Date

2023-08-30

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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