SMTL ID : 9cv3.1

Crystal structure of the metallo-beta-lactamase VIM-20 with L-captopril

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.51 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.91, H.93, H.156 Ligands: ZN.2, X8Z.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.91, A:H.93, A:H.156 ZN.2: 6 residues within 4Å: Chain A: D.95, R.96, C.175, H.217 Ligands: ZN.1, X8Z.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.95, A:C.175, A:H.217 ZN.3: 3 residues within 4Å: Chain A: H.228 Ligands: ACT.5, ACT.6 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Ligand interactions Metal complexes: A:H.228, ACT.5, ACT.6

1 x X8Z: L-CAPTOPRIL(Non-covalent)

X8Z.4: 12 residues within 4Å: Chain A: F.39, Y.44, W.64, H.93, D.95, H.156, C.175, N.187, H.217 Ligands: ZN.1, ZN.2, ACT.7 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:F.39, A:F.39, A:Y.44, A:Y.44, A:W.64, A:W.64 Hydrogen bonds: A:N.187

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.5: 6 residues within 4Å: Chain A: D.224, K.227, H.228, N.231 Ligands: ZN.3, ACT.6 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:K.227 Hydrogen bonds: A:N.231 Salt bridges: A:H.228 ACT.6: 5 residues within 4Å: Chain A: T.183, H.228, N.231 Ligands: ZN.3, ACT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.231 Hydrogen bonds: A:N.231 Salt bridges: A:H.228 ACT.7: 6 residues within 4Å: Chain A: H.156, Y.178, G.186, N.187, H.217 Ligands: X8Z.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.187 Water bridges: A:Y.178 Salt bridges: A:H.156, A:R.182

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Silwal, S.B. et al., Mutation of an active site-adjacent residue in VIM indirectly dictates interactions with and blunts inhibition by D-captopril. J.Inorg.Biochem. (2025)

Release Date

2025-07-09

Peptides

Metallo-beta-lactamase VIM-20: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase VIM-20

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