› 6lj0

X-ray diffraction
1.2Å resolution

Crystal structure of NDM-1 in complex with D-captopril derivative wss02122

Released:
DOI: 10.2210/pdb6lj0/pdb
PDB entry 6lj0 coloured by chain, front view.
PDB entry 6lj0 coloured by chain, side view.
PDB entry 6lj0 coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
Structure-guided optimization of D-captopril for discovery of potent NDM-1 inhibitors.
Ma G, Wang S, Wu K, Zhang W, Ahmad A, Hao Q, Lei X, Zhang H
Bioorg Med Chem 29 115902 (2021)
PMID: 33302045

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-504410 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase type 2 Chain: A
Molecule details ›
Chain: A
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

Ligands and Environments

2 bound ligands:
Ligand EER 1 x EER
Ligand ZN 2 x ZN
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: P21
Unit cell:
a: 41.818Å b: 60.06Å c: 42.169Å
α: 90° β: 98.06° γ: 90°
R-values:
R R work R free
0.154 0.153 0.174
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

2 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)
1 more

1 mention without citation

Integrating Siderophore Substructures in Thiol-Based Metallo-β-Lactamase Inhibitors.
Rotter et al. (2023)