SMTL ID : 7wpn.1

Methionyl-tRNA synthetase from Staphylococcus aureus complexed with a phenylbenzimidazole inhibitor and ATP

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

ATP.1: 19 residues within 4Å: Chain A: P.21, Y.23, H.30, G.32, H.33, S.36, A.280, E.282, I.283, H.309, G.310, W.311, I.312, K.318, M.319, S.320, K.321, S.322 Ligands: 29I.3 17 PLIP interactions: 17 interactions with chain A Hydrogen bonds: A:S.36, A:A.280, A:E.282, A:I.312, A:K.318, A:M.319, A:M.319, A:S.320, A:K.321, A:S.322 Salt bridges: A:H.30, A:H.33, A:K.318, A:K.318, A:K.321, A:K.321 pi-Stacking: A:H.33

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

EDO.2: 2 residues within 4Å: Chain A: Y.245 Ligands: 29I.3 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.245

1 x 29I: (phenylmethyl) N-[(2R)-2-[2-(4-bromanyl-3-oxidanyl-phenyl)-5-(methylcarbamoyl)benzimidazol-1-yl]-2-(3,4-dimethoxyphenyl)ethyl]carbamate(Non-covalent)

29I.3: 20 residues within 4Å: Chain A: I.22, Y.24, D.61, H.63, G.64, K.66, F.230, V.244, Y.245, V.246, W.247, D.249, A.250, L.251, Y.254, I.283, F.286, H.287 Ligands: ATP.1, EDO.2 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.22, A:Y.24, A:Y.24, A:K.66, A:F.230, A:Y.245, A:V.246, A:A.250, A:L.251, A:F.286, A:F.286 Hydrogen bonds: A:D.61, A:D.61, A:H.63 Water bridges: A:Y.24, A:E.62 pi-Stacking: A:Y.24 Halogen bonds: A:V.244

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 5 residues within 4Å: Chain A: H.63, T.107, K.112, W.232, G.233 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:W.232 Salt bridges: A:H.63, A:K.112

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yi, J. et al., Fragment screening and structural analyses highlight the ATP-assisted ligand binding for inhibitor discovery against type 1 methionyl-tRNA synthetase. Nucleic Acids Res. (2022)

Release Date

2022-04-27

Peptides

Methionine--tRNA ligase: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Methionine--tRNA ligase

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