SMTL ID : 5a87.1 (1 other biounit)

Crystal structure of the metallo-beta-lactamase VIM-5

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.1: 8 residues within 4Å: Chain A: F.44, W.69, H.98, D.100, N.192, H.222 Ligands: ZN.2, ZN.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.192 Water bridges: A:H.161, A:N.192, A:N.192 GOL.3: 8 residues within 4Å: Chain A: S.118, S.120, T.121, L.140, S.141, Y.156, D.164, L.166 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.118, A:T.121, A:S.141, A:D.164 GOL.5: 3 residues within 4Å: Chain A: D.99, G.129, N.130 6 PLIP interactions: 6 interactions with chain A Water bridges: A:D.99, A:D.99, A:G.129, A:G.129, A:N.130, A:E.131

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: H.96, H.98, D.100, H.161 Ligands: GOL.1, ZN.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.96, A:H.98, A:H.161, H2O.5 ZN.4: 6 residues within 4Å: Chain A: D.100, R.101, C.180, H.222 Ligands: GOL.1, ZN.2 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:D.100, A:C.180, A:H.222, H2O.5, H2O.7 ZN.6: 1 residues within 4Å: Chain A: H.135 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.135, H2O.9, H2O.9

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Makena, A. et al., Comparison of Verona Integron-Borne Metallo-beta-Lactamase (VIM) Variants Reveals Differences in Stability and Inhibition Profiles. Antimicrob. Agents Chemother. (2015)

Release Date

2015-12-23

Peptides

METALLO-BETA-LACTAMASE VIM-5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

METALLO-BETA-LACTAMASE VIM-5

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