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

Structure of metallo beta lactamase VIM-2 with cyclic boronate APC308.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.41 Å

Oligo State

monomer

Ligands

1 x KDZ: (3~{R})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid(Non-covalent)

KDZ.1: 16 residues within 4Å: Chain A: F.38, Y.43, W.63, H.90, H.92, D.94, H.155, C.174, G.185, N.186, A.188, D.189, H.216 Ligands: KL8.2, ZN.3, ZN.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.43, A:W.63, A:W.63, A:N.186, A:A.188 Hydrogen bonds: A:N.186, A:N.186 Salt bridges: A:H.155, A:H.216 pi-Stacking: A:F.38 pi-Cation interactions: A:H.216

1 x KL8: (3~{S})-2,2-bis(oxidanyl)-3-(phenylmethylsulfanyl)-3,4-dihydro-1,2-benzoxaborinin-2-ium-8-carboxylic acid(Non-covalent)

KL8.2: 15 residues within 4Å: Chain A: F.38, Y.43, W.63, H.90, H.92, D.93, D.94, H.155, C.174, G.185, N.186, H.216 Ligands: KDZ.1, ZN.3, ZN.5 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.38, A:F.38, A:Y.43, A:W.63, A:W.63 Hydrogen bonds: A:N.186 Salt bridges: A:H.155, A:H.216 pi-Cation interactions: A:H.216

3 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.90, H.92, H.155 Ligands: KDZ.1, KL8.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.4: 1 residues within 4Å: Chain A: H.129 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.129 ZN.5: 6 residues within 4Å: Chain A: D.94, R.95, C.174, H.216 Ligands: KDZ.1, KL8.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216

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

CL.6: 3 residues within 4Å: Chain A: H.227, N.230 Ligands: CL.7 Ligand excluded by PLIP CL.7: 2 residues within 4Å: Chain A: H.227 Ligands: CL.6 Ligand excluded by PLIP

2 x MG: MAGNESIUM ION(Non-covalent)

MG.8: 1 residues within 4Å: Chain A: G.7 No protein-ligand interaction detected (PLIP) MG.9: 1 residues within 4Å: Chain A: S.13 No protein-ligand interaction detected (PLIP)

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.10: 4 residues within 4Å: Chain A: P.82, V.83, A.105, V.107 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:V.83 Water bridges: A:L.81, A:V.83, A:G.106

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Parkova, A. et al., Broad Spectrum beta-Lactamase Inhibition by a Thioether Substituted Bicyclic Boronate. Acs Infect Dis. (2020)

Release Date

2020-03-25

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-lactamase VIM-2

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