SMTL ID : 8skp.1

X-ray structure of the NDM-4 beta-lactamase from Klebsiella pneumonia in complex with 1-hydroxypyridine-2(1H)-thione-6-carboxylic acid

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 7 residues within 4Å: Chain A: H.80, H.82, D.84, H.149, C.168 Ligands: ZN.2, WAF.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.80, A:H.82, A:H.149, H2O.2 ZN.2: 5 residues within 4Å: Chain A: D.84, C.168, H.210 Ligands: ZN.1, WAF.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:D.84, A:C.168, A:H.210, H2O.2

1 x WAF: 1-hydroxy-6-sulfanylidene-1,6-dihydropyridine-2-carboxylic acid(Non-covalent)

WAF.3: 14 residues within 4Å: Chain A: M.27, F.30, V.33, W.53, D.84, H.149, C.168, K.171, L.178, G.179, N.180, H.210 Ligands: ZN.1, ZN.2 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.30, A:V.33 Hydrogen bonds: A:N.180, A:N.180 Water bridges: A:K.171, A:K.171 Salt bridges: A:H.149, A:K.171 pi-Cation interactions: A:H.210

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 4 residues within 4Å: Chain A: Q.13, L.14, A.15, P.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:A.15

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Thoden, J.B. et al., Characterization of a novel inhibitor for the New Delhi metallo-beta-lactamase-4: Implications for drug design and combating bacterial drug resistance. J.Biol.Chem. (2023)

Release Date

2023-08-23

Peptides

Metallo-beta-lactamase type 2: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Metallo-beta-lactamase type 2

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