SMTL ID : 7a5z.1

Structure of VIM-2 metallo-beta-lactamase with hydrolysed Faropenem imine product

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.29 Å

Oligo State

monomer

Ligands

1 x QZH: (5~{Z})-2-[1,3-bis(oxidanyl)-1-oxidanylidene-butan-2-yl]-5-(4-oxidanylbutylidene)-2~{H}-1,3-thiazole-4-carboxylic acid(Non-covalent)

QZH.1: 18 residues within 4Å: Chain A: F.38, D.39, Y.43, W.63, H.90, H.92, D.93, D.94, H.155, C.174, Y.177, R.181, G.185, N.186, H.216 Ligands: ZN.3, ZN.4, NA.8 16 PLIP interactions: 16 interactions with chain A Hydrophobic interactions: A:F.38, A:F.38, A:Y.43, A:W.63, A:N.186 Hydrogen bonds: A:D.93, A:D.94, A:N.186, A:N.186 Water bridges: A:H.155, A:H.155 Salt bridges: A:H.90, A:H.92, A:H.155, A:H.155, A:H.216

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: CL.5, CL.6 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.129 ZN.3: 5 residues within 4Å: Chain A: H.90, H.92, H.155, C.174 Ligands: QZH.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.4: 5 residues within 4Å: Chain A: D.94, R.95, C.174, H.216 Ligands: QZH.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216

2 x CL: CHLORIDE ION(Non-functional Binders)

CL.5: 5 residues within 4Å: Chain A: A.108, T.128, H.129 Ligands: ZN.2, CL.6 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: ZN.2, CL.5 Ligand excluded by PLIP

1 x MG: MAGNESIUM ION(Non-covalent)

MG.7: 4 residues within 4Å: Chain A: S.112, P.113, S.114, S.135 No protein-ligand interaction detected (PLIP)

1 x NA: SODIUM ION(Non-functional Binders)

NA.8: 4 residues within 4Å: Chain A: H.92, D.93, N.124 Ligands: QZH.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.93, A:N.124 Water bridges: A:D.93, A:D.93, A:D.93

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucic, A. et al., Faropenem reacts with serine and metallo-beta-lactamases to give multiple products. Eur.J.Med.Chem. (2021)

Release Date

2021-02-24

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase VIM-2

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