SMTL ID : 8sk2.1

X-ray structure of the NDM-4 beta-lactamase from Klebsiella pneumonia, apo form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 6 residues within 4Å: Chain A: H.119, H.121, D.123, H.188, C.207 Ligands: ZN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.119, A:H.121, A:H.188, H2O.3 ZN.2: 4 residues within 4Å: Chain A: D.123, C.207, H.249 Ligands: ZN.1 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.123, A:C.207, A:H.249, H2O.3, H2O.3, H2O.6

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

EDO.3: 6 residues within 4Å: Chain A: G.41, Q.43, F.50, R.51, Q.52, W.58 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.52 Water bridges: A:Q.43 EDO.4: 2 residues within 4Å: Chain A: W.58, E.107 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.107, A:E.107 Water bridges: A:Q.43

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