SMTL ID : 8pjm.1

Metallo beta-lactamase VIM2 with compound AK4

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.44 Å

Oligo State

monomer

Ligands

1 x ZJ5: ~{N}-[[(3~{R})-1,1-bis(oxidanyl)-3~{H}-2,1$l^{4}-benzoxaborol-3-yl]methyl]methanesulfonamide(Non-covalent)

ZJ5.1: 15 residues within 4Å: Chain A: F.38, Y.43, W.63, H.90, H.92, D.94, H.155, C.174, R.181, G.185, N.186, H.216 Ligands: ZN.2, ZN.3, CL.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.63 Hydrogen bonds: A:D.94, A:R.181, A:N.186 pi-Stacking: A:F.38

3 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: H.90, H.92, H.155 Ligands: ZJ5.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.3: 5 residues within 4Å: Chain A: D.94, R.95, C.174, H.216 Ligands: ZJ5.1 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216 ZN.4: 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

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

CL.5: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: ZN.4, CL.6 Ligand excluded by PLIP CL.6: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: ZN.4, CL.5 Ligand excluded by PLIP CL.7: 4 residues within 4Å: Chain A: H.155, R.181 Ligands: ZJ5.1, NA.8 Ligand excluded by PLIP

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

NA.8: 5 residues within 4Å: Chain A: H.155, Y.177, R.181, W.195 Ligands: CL.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Y.177, A:Y.177, A:R.181 Water bridges: A:R.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kranjc, A. et al., Metallo beta-lactamase VIM2 with compound AK4. To Be Published

Release Date

2023-08-16

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
AAAA

Beta-lactamase VIM-2

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