SMTL ID : 7wpx.1

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

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

ATP.1: 23 residues within 4Å: Chain A: P.21, Y.23, Y.24, S.26, H.30, G.32, H.33, S.36, K.66, 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 Ligands: 2I3.2 24 PLIP interactions: 24 interactions with chain A Hydrogen bonds: A:Y.24, A:S.26, A:S.36, A:A.280, A:E.282, A:I.312, A:K.318, A:M.319, A:M.319, A:K.321, A:S.322, A:S.322 Water bridges: A:K.318, A:S.320 Salt bridges: A:H.33, A:H.33, A:K.66, A:K.66, A:K.318, A:K.318, A:K.321, A:K.321, A:K.321 pi-Stacking: A:H.33

1 x 2I3: 6-chloranylimidazo[2,1-b][1,3]thiazole(Non-covalent)

2I3.2: 12 residues within 4Å: Chain A: P.21, I.22, Y.24, D.61, W.247, A.250, L.251, N.253, Y.254, I.283, H.287 Ligands: ATP.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:I.22, A:Y.254 pi-Stacking: A:Y.24

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

EDO.3: 6 residues within 4Å: Chain A: N.28, L.29, M.85, G.88, I.89, N.330 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.85, A:N.330

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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