› 6d1c

X-ray diffraction
1.25Å resolution

Crystal structure of NDM-1 complexed with compound 3

Released:
DOI: 10.2210/pdb6d1c/pdb
PDB entry 6d1c coloured by chain, front view.
PDB entry 6d1c coloured by chain, side view.
PDB entry 6d1c coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Pemberton OA, Jaishankar P, Akhtar A, Adams JL, Shaw LN, Renslo AR, Chen Y
J Med Chem 62 8480-8496 (2019)
PMID: 31483651

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

3 bound ligands:
Ligand ZN 2 x ZN
Ligand VKE 1 x VKE
Ligand ACT 2 x ACT
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 22-BM
Spacegroup: P21
Unit cell:
a: 41.68Å b: 59.96Å c: 41.95Å
α: 90° β: 97.9° γ: 90°
R-values:
R R work R free
0.147 0.146 0.174
Expression system: Escherichia coli BL21(DE3)

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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

1 mention without citation

Heteroaryl Phosphonates as Noncovalent Inhibitors of Both Serine- and Metallocarbapenemases.
Pemberton et al. (2019)