SMTL ID : 5n4t.1 (1 other biounit)

VIM-2 metallo-beta-lactamase in complex with ((S)-3-mercapto-2-methylpropanoyl)-L-tryptophan (Compound 4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.16 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 5 residues within 4Å: Chain A: H.85, H.87, H.150 Ligands: ZN.2, R59.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.85, A:H.87, A:H.150 ZN.2: 6 residues within 4Å: Chain A: D.89, R.90, C.169, H.211 Ligands: ZN.1, R59.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.89, A:C.169, A:H.211 ZN.3: 3 residues within 4Å: Chain A: H.222 Ligands: FMT.5, BEZ.7 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.222

1 x R59: (2~{S})-3-(1~{H}-indol-3-yl)-2-[[(2~{S})-2-methyl-3-sulfanyl-propanoyl]amino]propanoic acid(Non-covalent)

R59.4: 13 residues within 4Å: Chain A: Y.38, W.58, H.85, H.87, D.89, H.150, C.169, R.176, G.180, N.181, H.211 Ligands: ZN.1, ZN.2 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:Y.38, A:Y.38, A:W.58, A:H.211 Hydrogen bonds: A:N.181, A:N.181 Water bridges: A:R.176, A:R.176, A:A.179 Salt bridges: A:H.150, A:R.176, A:H.211 pi-Cation interactions: A:R.176, A:R.176

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

FMT.5: 4 residues within 4Å: Chain A: H.222, N.225 Ligands: ZN.3, BEZ.7 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.225 FMT.6: 3 residues within 4Å: Chain A: P.108, S.109, R.112 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.112 Water bridges: A:S.109

1 x BEZ: BENZOIC ACID(Non-covalent)

BEZ.7: 5 residues within 4Å: Chain A: T.177, H.222, N.225 Ligands: ZN.3, FMT.5 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:N.225 Hydrogen bonds: A:N.225 Salt bridges: A:H.222

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Li, G.B. et al., Crystallographic analyses of isoquinoline complexes reveal a new mode of metallo-beta-lactamase inhibition. Chem. Commun. (Camb.) (2017)

Release Date

2017-05-17

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Beta-lactamase VIM-2

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