SMTL ID : 6kzn.2 (1 other biounit)

Crystal Structure Of VIM-2 Metallo-beta-lactamase In Complex With Inhibitor X2

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: D.92, R.93, C.172, H.214 Ligands: ZN.3, E1C.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.92, A:C.172, A:H.214 ZN.2: 3 residues within 4Å: Chain A: H.127 Ligands: FMT.4, FMT.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.127 ZN.3: 6 residues within 4Å: Chain A: H.88, H.90, D.92, H.153 Ligands: ZN.1, E1C.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.88, A:H.90, A:H.153

2 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 4 residues within 4Å: Chain A: A.106, H.127 Ligands: ZN.2, FMT.5 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.108 FMT.5: 4 residues within 4Å: Chain A: T.126, H.127 Ligands: ZN.2, FMT.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:T.126

1 x E1C: 2,5-diethyl-1-methyl-4-sulfamoyl-pyrrole-3-carboxylic acid(Non-covalent)

E1C.6: 13 residues within 4Å: Chain A: Y.41, W.61, H.88, H.90, D.92, H.153, C.172, R.179, G.183, N.184, H.214 Ligands: ZN.1, ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:Y.41, A:Y.41, A:W.61 Hydrogen bonds: A:N.184, A:N.184 Water bridges: A:G.183 Salt bridges: A:H.153, A:H.214 pi-Stacking: A:H.214

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wachino, J.I. et al., Sulfamoyl Heteroarylcarboxylic Acids as Promising Metallo-beta-Lactamase Inhibitors for Controlling Bacterial Carbapenem Resistance. Mbio (2020)

Release Date

2020-02-19

Peptides

Beta-lactamase class B VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-lactamase class B VIM-2

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