SMTL ID : 7ot3.1

Human Prolyl-tRNA Synthetase in Complex with L-proline and Compound 3b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.53 Å

Oligo State

homo-dimer

Ligands

2 x PRO: PROLINE(Non-covalent)

PRO.1: 13 residues within 4Å: Chain A: T.121, E.123, R.152, W.169, E.171, H.173, F.216, T.240, H.242, S.272, W.273, G.274 Ligands: 0W4.2 8 PLIP interactions: 1 Ligand-Ligand interactions, 7 interactions with chain A Hydrogen bonds: P.1, A:T.121, A:T.240, A:S.272 Hydrophobic interactions: A:W.169, A:E.171 Salt bridges: A:R.152, A:H.242 PRO.7: 13 residues within 4Å: Chain B: T.121, E.123, R.152, W.169, E.171, H.173, F.216, T.240, H.242, S.272, W.273, G.274 Ligands: 0W4.8 11 PLIP interactions: 9 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.169, B:E.171 Hydrogen bonds: B:T.121, B:T.121, B:T.121, B:T.240, B:S.272, P.7, P.7 Salt bridges: B:R.152, B:H.242

2 x 0W4: ~{N}-[(2-chlorophenyl)methyl]-3-[(2-chlorophenyl)methylamino]pyrazine-2-carboxamide(Non-covalent)

0W4.2: 18 residues within 4Å: Chain A: R.152, E.154, K.156, F.161, L.162, R.163, T.164, R.165, F.167, W.169, Q.237, G.238, G.239, T.240, G.274, T.276, R.278 Ligands: PRO.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:E.154, A:R.163, A:R.165, A:W.169, A:T.276 Hydrogen bonds: A:T.164, A:T.164, A:T.276 pi-Stacking: A:F.167 Halogen bonds: A:Q.237 0W4.8: 18 residues within 4Å: Chain B: R.152, E.154, K.156, F.161, L.162, R.163, T.164, R.165, F.167, W.169, Q.237, G.238, G.239, T.240, G.274, T.276, R.278 Ligands: PRO.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:E.154, B:E.154, B:R.163, B:R.165, B:W.169, B:T.276 Hydrogen bonds: B:T.164, B:T.164, B:T.276 pi-Stacking: B:F.167 Halogen bonds: B:Q.237

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.448, C.453, C.495, C.497 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.448, A:C.453, A:C.495, A:C.497 ZN.9: 4 residues within 4Å: Chain B: C.448, C.453, C.495, C.497 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.448, B:C.453, B:C.495, B:C.497

4 x SR: STRONTIUM ION(Non-functional Binders)

SR.4: 1 residues within 4Å: Chain A: D.220 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.220, H2O.1, H2O.1 SR.5: 1 residues within 4Å: Chain A: G.72 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:G.72, H2O.1, H2O.1, H2O.1 SR.6: 2 residues within 4Å: Chain A: D.96, E.100 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.96, A:D.96, H2O.1 SR.10: 1 residues within 4Å: Chain B: D.96 1 PLIP interactions: 1 interactions with chain B Metal complexes: B:D.96

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Pang, L. et al., Towards Novel 3-Aminopyrazinamide-Based Prolyl-tRNA Synthetase Inhibitors: In Silico Modelling, Thermal Shift Assay and Structural Studies. Int J Mol Sci (2021)

Release Date

2021-07-28

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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