SMTL ID : 6ew3.1 (1 other biounit)

Crystal structure of the metallo-beta-lactamase VIM-2 with ML302F

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.14 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.83, H.85, H.148 Ligands: ZN.2, S3C.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.85, A:H.148 ZN.2: 6 residues within 4Å: Chain A: D.87, R.88, C.167, H.209 Ligands: ZN.1, S3C.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.87, A:C.167, A:H.209 ZN.3: 3 residues within 4Å: Chain A: H.122 Ligands: FMT.4, FMT.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.122

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

FMT.4: 7 residues within 4Å: Chain A: V.100, A.101, T.102, T.121, H.122 Ligands: ZN.3, FMT.5 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:T.102, A:T.121 FMT.5: 4 residues within 4Å: Chain A: A.101, H.122 Ligands: ZN.3, FMT.4 No protein-ligand interaction detected (PLIP)

1 x S3C: (2Z)-2-sulfanyl-3-(2,3,6-trichlorophenyl)prop-2-enoic acid(Non-covalent)

S3C.6: 14 residues within 4Å: Chain A: F.31, W.56, H.83, H.85, D.86, D.87, H.148, C.167, N.179, H.209 Ligands: ZN.1, ZN.2, DMS.7, DMS.8 4 PLIP interactions: 4 interactions with chain A Salt bridges: A:H.148, A:H.209 pi-Stacking: A:H.85 Halogen bonds: A:N.179

2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.7: 5 residues within 4Å: Chain A: Y.36, R.174, H.209 Ligands: S3C.6, DMS.8 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.174 pi-Cation interactions: A:H.209 DMS.8: 5 residues within 4Å: Chain A: F.31, Y.36, N.179 Ligands: S3C.6, DMS.7 3 PLIP interactions: 3 interactions with chain A Water bridges: A:N.179 pi-Cation interactions: A:F.31, A:Y.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, D. et al., Structure activity relationship studies on rhodanines and derived enethiol inhibitors of metallo-beta-lactamases. Bioorg. Med. Chem. (2018)

Release Date

2018-10-03

Peptides

Metallo-beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase VIM-2

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