› 6efj

X-ray diffraction
1.65Å resolution

Crystal structure of NDM-1 with compound 9

Released:
DOI: 10.2210/pdb6efj/pdb
PDB entry 6efj coloured by chain, front view.
PDB entry 6efj coloured by chain, side view.
PDB entry 6efj coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
Active-Site Druggability of Carbapenemases and Broad-Spectrum Inhibitor Discovery.
Torelli NJ, Akhtar A, DeFrees K, Jaishankar P, Pemberton OA, Zhang X, Johnson C, Renslo AR, Chen Y
ACS Infect Dis 5 1013-1021 (2019)
PMID: 30942078

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 Chain: A
Molecule details ›
Chain: A
Length: 233 amino acids
Theoretical weight: 24.6 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: C7C422 (Residues: 42-270; Coverage: 95%)
Gene name: blaNDM-1
Sequence domains: Metallo-beta-lactamase superfamily

Ligands and Environments

2 bound ligands:
Ligand ZN 2 x ZN
Ligand O5E 1 x O5E
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 19-BM
Spacegroup: P21
Unit cell:
a: 41.98Å b: 58.77Å c: 41.98Å
α: 90° β: 97.48° γ: 90°
R-values:
R R work R free
0.18 0.176 0.222
Expression system: Escherichia coli BL21(DE3)

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Citations

1 review citation

Can We Exploit β-Lactamases Intrinsic Dynamics for Designing More Effective Inhibitors?
Gianquinto et al. (2020)
5 other articles