SMTL ID : 6p8t.1 (1 other biounit)

Acinetobacter baumannii tRNA synthetase in complex with compound 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.15 Å

Oligo State

hetero-2-2-mer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: N.165, D.454, E.463 Chain C: E.255 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain A Metal complexes: C:E.255, A:E.463 MG.2: 5 residues within 4Å: Chain B: N.165, D.454, D.460, E.463 Chain D: E.255 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain B Metal complexes: D:E.255, B:E.463

2 x NO4: N-benzyl-2-(cyclohex-1-en-1-yl)ethan-1-amine(Non-covalent)

NO4.3: 14 residues within 4Å: Chain C: L.146, S.174, Q.177, I.178, M.181, E.213, F.251, F.253, G.274, C.275, V.278, A.297, F.298, G.299 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:L.146, C:I.178, C:F.253, C:F.253, C:V.278, C:A.297 Hydrogen bonds: C:Q.177, C:E.213 pi-Stacking: C:F.251, C:F.253 NO4.4: 16 residues within 4Å: Chain D: L.146, S.174, Q.177, I.178, M.181, E.213, L.215, F.251, F.253, G.274, C.275, V.278, V.282, A.297, F.298, G.299 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:L.146, D:Q.177, D:I.178, D:L.215, D:F.251, D:F.253, D:F.253, D:V.278, D:V.282 pi-Stacking: D:F.253

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Baidin, V. et al., Simple Secondary Amines Inhibit Growth of Gram-Negative Bacteria through Highly Selective Binding to Phenylalanyl-tRNA Synthetase. J.Am.Chem.Soc. (2021)

Release Date

2020-11-18

Peptides

Phenylalanine--tRNA ligase beta subunit: AB
Phenylalanine--tRNA ligase alpha subunit: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Phenylalanine--tRNA ligase beta subunit

Phenylalanine--tRNA ligase alpha subunit

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