SMTL ID : 8xm4.1

Methionyl-tRNA synthetase from Staphylococcus aureus in complex with chlorhexidine and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.67 Å

Oligo State

monomer

Ligands

1 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.1: 21 residues within 4Å: Chain A: P.21, I.22, Y.23, Y.24, H.30, G.32, H.33, Y.35, S.36, M.279, A.280, E.282, I.283, H.309, G.310, W.311, I.312, K.318, M.319, K.321 Ligands: XC9.2 18 PLIP interactions: 18 interactions with chain A Hydrogen bonds: A:I.22, A:Y.24, A:S.36, A:A.280, A:E.282, A:I.312, A:I.312, A:K.318, A:M.319 Water bridges: A:D.61, A:E.282 Salt bridges: A:H.33, A:H.33, A:K.318, A:K.321, A:K.321, A:K.321 pi-Stacking: A:H.33

1 x XC9: 1-[6-[azanylidene-[[azanylidene-[[(4-chlorophenyl)amino]methyl]-$l^{4}-azanyl]methyl]-$l^{4}-azanyl]hexyl]-3-[~{N}-(4-chlorophenyl)carbamimidoyl]guanidine(Non-covalent)

XC9.2: 16 residues within 4Å: Chain A: Y.24, D.61, H.63, G.64, F.230, V.243, V.244, Y.245, V.246, W.247, D.249, L.251, I.283, F.286 Ligands: ATP.1, EDO.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:H.63, A:Y.245, A:V.246, A:V.246, A:W.247, A:I.283, A:F.286 Salt bridges: A:D.61 pi-Cation interactions: A:Y.24

4 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 8 residues within 4Å: Chain A: P.21, I.22, A.250, N.253, Y.254, I.283, H.287 Ligands: XC9.2 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:I.22, A:N.253, A:Y.254 Water bridges: A:I.22 EDO.4: 4 residues within 4Å: Chain A: E.132, Y.133, E.134, F.181 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.132, A:E.134 EDO.5: 5 residues within 4Å: Chain A: N.28, L.29, G.88, I.89, N.330 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.29, A:N.330 Water bridges: A:D.328, A:D.328 EDO.6: 4 residues within 4Å: Chain A: K.13, E.14, G.51, Y.52 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.14, A:G.51

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lu, F. et al., Biochemical and structural characterization of chlorhexidine as an ATP-assisted inhibitor against type 1 methionyl-tRNA synthetase from Gram-positive bacteria. Eur.J.Med.Chem. (2024)

Release Date

2024-11-06

Peptides

Methionine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine--tRNA ligase

Related Entries With Identical Sequence