SMTL ID : 6y6j.1

VIM-2 in Complex with Biapenem Imine and Enamine Hydrolysis Products

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

monomer

Ligands

1 x OEN: Biapenem Imine hydrolysis product(Non-covalent)

OEN.1: 16 residues within 4Å: Chain A: F.31, Y.36, W.56, H.83, H.85, D.86, D.87, H.148, C.167, R.174, G.178, N.179, H.209 Ligands: OEQ.2, ZN.3, ZN.4 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.31, A:F.31, A:W.56, A:W.56 Hydrogen bonds: A:D.87, A:D.87, A:N.179 Water bridges: A:R.174, A:R.174, A:R.174, A:R.174 Salt bridges: A:H.83, A:H.85, A:H.148, A:H.148, A:R.174, A:H.209 pi-Cation interactions: A:R.174

1 x OEQ: Biapenem Enamine hydrolysis product(Non-covalent)

OEQ.2: 16 residues within 4Å: Chain A: F.31, Y.36, W.56, H.83, H.85, D.86, D.87, H.148, C.167, R.174, G.178, N.179, H.209 Ligands: OEN.1, ZN.3, ZN.4 19 PLIP interactions: 19 interactions with chain A Hydrophobic interactions: A:F.31, A:F.31, A:W.56, A:W.56 Hydrogen bonds: A:D.86, A:D.87, A:D.87, A:N.179 Water bridges: A:R.174, A:R.174, A:R.174, A:R.174, A:R.174 Salt bridges: A:H.83, A:H.85, A:H.148, A:H.148, A:R.174, A:H.209

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.83, H.85, H.148 Ligands: OEN.1, OEQ.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.83, A:H.85, A:H.148 ZN.4: 6 residues within 4Å: Chain A: D.87, R.88, C.167, H.209 Ligands: OEN.1, OEQ.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:D.87, A:C.167, A:H.209, OEQ.2 ZN.5: 4 residues within 4Å: Chain A: A.101, H.122 Ligands: CL.6, CL.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.122

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

CL.6: 4 residues within 4Å: Chain A: A.101, H.122 Ligands: ZN.5, CL.7 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: A.101, H.122 Ligands: ZN.5, CL.6 Ligand excluded by PLIP CL.8: 3 residues within 4Å: Chain A: H.85, D.86, N.117 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lucic, A. et al., Structure of metallo-beta-lactamase VIM-2 in complex with the imine and enamine form of hydrolysed Biapenem. To Be Published

Release Date

2021-03-31

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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