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

Structure of VIM-2 with 2-Mercaptomethyl-thiazolidine D-syn-1b

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

monomer

Ligands

3 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.90, D.94, R.95, C.174, H.216 Ligands: ZN.2, QST.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:D.94, A:C.174, A:H.216 ZN.2: 6 residues within 4Å: Chain A: H.90, H.92, H.155, C.174 Ligands: ZN.1, QST.6 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.90, A:H.92, A:H.155 ZN.3: 4 residues within 4Å: Chain A: A.108, H.129 Ligands: FMT.4, FMT.5 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.129

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

FMT.4: 7 residues within 4Å: Chain A: R.103, A.108, T.109, T.128, H.129 Ligands: ZN.3, FMT.5 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.109, A:T.128 Water bridges: A:T.109 FMT.5: 5 residues within 4Å: Chain A: A.108, Y.110, H.129 Ligands: ZN.3, FMT.4 1 PLIP interactions: 1 interactions with chain A Water bridges: A:Y.110

1 x QST: (2~{S},4~{S})-2-ethoxycarbonyl-5,5-dimethyl-2-(sulfanylmethyl)-1,3-thiazolidine-4-carboxylic acid(Non-covalent)

QST.6: 15 residues within 4Å: Chain A: F.38, Y.43, W.63, H.90, H.92, D.93, D.94, H.155, C.174, R.181, G.185, N.186, H.216 Ligands: ZN.1, ZN.2 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:Y.43, A:W.63, A:D.93 Hydrogen bonds: A:N.186, A:N.186 Water bridges: A:R.181 Salt bridges: A:R.181

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Rossi, M.A. et al., 2-Mercaptomethyl-thiazolidines use conserved aromatic-S interactions to achieve broad-range inhibition of metallo-beta-lactamases. Chem Sci (2021)

Release Date

2021-01-20

Peptides

Beta-lactamase VIM-2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Beta-lactamase VIM-2

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