› 5zge

X-ray diffraction
1Å resolution

Crystal structure of NDM-1 at pH5.5 (Bis-Tris) in complex with hydrolyzed ampicillin

Released:
DOI: 10.2210/pdb5zge/pdb
PDB entry 5zge coloured by chain, front view.
PDB entry 5zge coloured by chain, side view.
PDB entry 5zge coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
Active-Site Conformational Fluctuations Promote the Enzymatic Activity of NDM-1.
Zhang H, Ma G, Zhu Y, Zeng L, Ahmad A, Wang C, Pang B, Fang H, Zhao L, Hao Q
Antimicrob Agents Chemother 62 (2018)
PMID: 30150473

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-111680 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chains: A, B
Molecule details ›
Chains: A, B
Length: 242 amino acids
Theoretical weight: 25.63 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C7C422 (Residues: 29-270; Coverage: 100%)
Gene name: blaNDM-1
Sequence domains: Metallo-beta-lactamase superfamily
Structure domains: Ribonuclease Z/Hydroxyacylglutathione hydrolase-like

Ligands and Environments

3 bound ligands:
Ligand ZZ7 2 x ZZ7
Ligand ZN 4 x ZN
Ligand OH 2 x OH
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P212121
Unit cell:
a: 39.204Å b: 79.071Å c: 133.974Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.128 0.128 0.145
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

3 review citations

Metallo-β-lactamases in the Age of Multidrug Resistance: From Structure and Mechanism to Evolution, Dissemination, and Inhibitor Design.
Bahr et al. (2021)
2 more

12 mentions without citation

Bicyclic Boronate VNRX-5133 Inhibits Metallo- and Serine-β-Lactamases.
Krajnc et al. (2019)
11 more