SMTL ID : 8xm3.1

Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a chlorhexidine derivative and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.92 Å

Oligo State

monomer

Ligands

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

ATP.1: 20 residues within 4Å: Chain A: P.21, Y.23, 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, S.320, K.321, S.322 20 PLIP interactions: 20 interactions with chain A Hydrogen bonds: A:S.36, A:A.280, A:E.282, A:I.312, A:I.312, A:K.318, A:M.319, A:K.321, A:S.322 Water bridges: A:K.321, A:K.321 Salt bridges: A:H.30, A:H.33, A:H.33, A:K.318, A:K.318, A:K.321, A:K.321, A:K.321 pi-Stacking: A:H.33

2 x 01: 1-(4-chlorophenyl)-3-[~{N}-[4-[[~{N}-[~{N}-(4-chlorophenyl)carbamimidoyl]carbamimidoyl]amino]butyl]carbamimidoyl]guanidine

01.2: 13 residues within 4Å: Chain A: Y.24, D.61, H.63, G.64, F.230, V.244, Y.245, V.246, W.247, D.249, A.250, L.251, F.286 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:H.63, A:Y.245, A:V.246, A:W.247, A:F.286 Water bridges: A:Y.144 Salt bridges: A:D.61 pi-Cation interactions: A:Y.24 01.3: 6 residues within 4Å: Chain A: D.189, L.192, D.196, N.209, N.213, K.217 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:L.192, A:K.217 Hydrogen bonds: A:L.192, A:N.209 Salt bridges: A:D.189, A:D.196

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

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