SMTL ID : 4hvc.1

Crystal structure of human prolyl-tRNA synthetase in complex with halofuginone and ATP analogue

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.1: 16 residues within 4Å: Chain A: R.159, E.161, F.168, L.169, R.170, T.171, F.174, W.176, Q.244, G.245, G.246, T.247, T.283, R.285 Ligands: HFG.2, MG.3 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:R.159, A:E.161, A:K.163, A:R.170, A:R.170, A:T.171, A:Q.244, A:Q.244, A:T.247, A:T.247, A:T.283, A:R.285 Water bridges: A:H.249, A:T.283 Salt bridges: A:R.159 pi-Stacking: A:F.174, A:F.174 pi-Cation interactions: A:R.285 ANP.5: 16 residues within 4Å: Chain B: R.159, E.161, F.168, L.169, R.170, T.171, F.174, W.176, Q.244, G.245, G.246, T.247, T.283, R.285 Ligands: HFG.6, MG.7 18 PLIP interactions: 18 interactions with chain B Hydrogen bonds: B:R.159, B:E.161, B:R.170, B:R.170, B:T.171, B:Q.244, B:Q.244, B:T.247, B:T.247, B:T.283, B:R.285, B:R.285 Water bridges: B:K.163, B:T.283 Salt bridges: B:R.159 pi-Stacking: B:F.174, B:F.174 pi-Cation interactions: B:R.285

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

HFG.2: 18 residues within 4Å: Chain A: H.100, F.104, E.107, V.108, P.127, T.128, E.130, R.159, W.176, E.178, H.180, F.223, T.247, H.249, S.279, W.280, G.281 Ligands: ANP.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:H.100, A:T.128, A:W.176, A:E.178, A:F.223 Hydrogen bonds: A:T.128, A:R.159, A:S.279 Water bridges: A:R.159, A:H.249 pi-Stacking: A:F.104, A:F.104 HFG.6: 19 residues within 4Å: Chain B: L.94, H.100, F.104, E.107, V.108, P.127, T.128, E.130, R.159, W.176, E.178, H.180, F.223, T.247, H.249, S.279, W.280, G.281 Ligands: ANP.5 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:H.100, B:P.127, B:T.128, B:W.176, B:E.178, B:F.223 Hydrogen bonds: B:T.128, B:T.128, B:R.159, B:S.279 Water bridges: B:R.159, B:H.249 pi-Stacking: B:F.104, B:F.104

2 x MG: MAGNESIUM ION(Non-covalent)

MG.3: 3 residues within 4Å: Chain A: R.159, R.170 Ligands: ANP.1 No protein-ligand interaction detected (PLIP) MG.7: 2 residues within 4Å: Chain B: R.159 Ligands: ANP.5 No protein-ligand interaction detected (PLIP)

2 x ZN: ZINC ION(Non-covalent)

ZN.4: 4 residues within 4Å: Chain A: C.455, C.460, C.502, C.504 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.455, A:C.460, A:C.502 ZN.8: 4 residues within 4Å: Chain B: C.455, C.460, C.502, C.504 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:C.455, B:C.460, B:C.502

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhou, H. et al., ATP-directed capture of bioactive herbal-based medicine on human tRNA synthetase. Nature (2012)

Release Date

2013-01-02

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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