SMTL ID : 5vad.1

Crystal structure of human Prolyl-tRNA synthetase (PRS) in complex with inhibitor

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.36 Å

Oligo State

homo-dimer

Ligands

2 x 91Y: 3-[(cyclohexanecarbonyl)amino]-N-(2,3-dihydro-1H-inden-2-yl)pyrazine-2-carboxamide(Non-covalent)

91Y.1: 16 residues within 4Å: Chain A: R.156, E.158, K.160, H.161, F.165, L.166, R.167, T.168, F.171, W.173, Q.241, T.244, G.278, T.280, R.282 Ligands: PRO.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.156, A:E.158, A:E.158, A:K.160, A:R.167, A:W.173 Hydrogen bonds: A:T.168, A:T.168, A:R.282 pi-Stacking: A:F.171 91Y.4: 16 residues within 4Å: Chain B: R.156, E.158, K.160, H.161, F.165, L.166, R.167, T.168, F.171, W.173, Q.241, T.244, G.278, T.280, R.282 Ligands: PRO.5 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:R.156, B:E.158, B:K.160, B:R.167, B:W.173, B:T.280 Hydrogen bonds: B:T.168, B:T.168, B:R.282 pi-Stacking: B:F.171

2 x PRO: PROLINE(Non-covalent)

PRO.2: 13 residues within 4Å: Chain A: T.125, E.127, R.156, W.173, E.175, H.177, F.220, T.244, H.246, S.276, W.277, G.278 Ligands: 91Y.1 9 PLIP interactions: 8 interactions with chain A, 1 Ligand-Ligand interactions Hydrophobic interactions: A:W.173, A:E.175 Hydrogen bonds: A:T.125, A:T.244, A:S.276, P.2 Water bridges: A:R.156 Salt bridges: A:R.156, A:H.246 PRO.5: 12 residues within 4Å: Chain B: T.125, E.127, R.156, W.173, E.175, H.177, F.220, H.246, S.276, W.277, G.278 Ligands: 91Y.4 9 PLIP interactions: 7 interactions with chain B, 2 Ligand-Ligand interactions Hydrophobic interactions: B:W.173, B:E.175 Hydrogen bonds: B:T.125, B:T.125, B:S.276, P.5, P.5 Salt bridges: B:R.156, B:H.246

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.452, C.457, C.499, C.501 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.452, A:C.457, A:C.499 ZN.6: 4 residues within 4Å: Chain B: C.452, C.457, C.499, C.501 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.452, B:C.457, B:C.499

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Adachi, R. et al., Discovery of a novel prolyl-tRNA synthetase inhibitor and elucidation of its binding mode to the ATP site in complex with l-proline. Biochem. Biophys. Res. Commun. (2017)

Release Date

2017-05-31

Peptides

Bifunctional glutamate/proline--tRNA ligase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Bifunctional glutamate/proline--tRNA ligase