SMTL ID : 7by6.1

Plasmodium vivax cytoplasmic Phenylalanyl-tRNA synthetase in complex with BRD1389

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.00 Å

Oligo State

hetero-2-2-mer

Ligands

2 x FB9: (3S,4R,8R,9R,10S)-N-(4-cyclopropyloxyphenyl)-10-(methoxymethyl)-3,4-bis(oxidanyl)-9-[4-(2-phenylethynyl)phenyl]-1,6-diazabicyclo[6.2.0]decane-6-carboxamide(Non-covalent)

FB9.1: 17 residues within 4Å: Chain A: R.173, Q.187, E.189, I.213, I.215, Y.227, E.246, V.247, N.249, S.250, A.271, W.272, G.273, L.274, S.275, R.278, P.279 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Q.187, A:I.213, A:V.247, A:V.247, A:L.274, A:R.278, A:P.279 Hydrogen bonds: A:E.246, A:S.275 pi-Stacking: A:Y.227 FB9.3: 17 residues within 4Å: Chain C: R.173, Q.187, E.189, I.213, I.215, Y.227, E.246, V.247, N.249, S.250, A.271, W.272, G.273, L.274, S.275, R.278, P.279 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:Q.187, C:I.213, C:V.247, C:V.247, C:L.274, C:R.278, C:P.279 Hydrogen bonds: C:E.246, C:S.275 pi-Stacking: C:Y.227

2 x MG: MAGNESIUM ION(Non-covalent)

MG.2: 4 residues within 4Å: Chain A: E.229 Chain B: N.55, D.353, E.362 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Metal complexes: A:E.229, B:E.362, B:E.362 MG.4: 4 residues within 4Å: Chain C: E.229 Chain D: N.55, D.353, E.362 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain C Metal complexes: D:E.362, D:E.362, C:E.229

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sharma, M. et al., Structural basis of malaria parasite phenylalanine tRNA-synthetase inhibition by bicyclic azetidines. Nat Commun (2021)

Release Date

2020-11-04

Peptides

Phenylalanyl-tRNA synthetase beta chain, putative: AC
Phenylalanyl-tRNA synthetase beta chain, putative: BD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

C
A

B
B

D
B

Phenylalanyl-tRNA synthetase beta chain, putative

Phenylalanyl-tRNA synthetase beta chain, putative