› 6tgd

X-ray diffraction
1.33Å resolution

Crystal structure of NDM-1 in complex with triazole-based inhibitor OP31

Released:
DOI: 10.2210/pdb6tgd/pdb
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PDB entry 6tgd coloured by chain, front view.
PDB entry 6tgd coloured by chain, side view.
PDB entry 6tgd coloured by chain, top view.
Source organism: Pseudomonas aeruginosa
Primary publication:
Virtual screening identifies broad-spectrum β-lactamase inhibitors with activity on clinically relevant serine- and metallo-carbapenemases.
Spyrakis F, Santucci M, Maso L, Cross S, Gianquinto E, Sannio F, Verdirosa F, De Luca F, Docquier JD, Cendron L, Tondi D, Venturelli A, Cruciani G, Costi MP
OpenAccess logo Sci Rep 10 12763 (2020)
PMID: 32728062

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-126005 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Metallo-beta-lactamase domain-containing protein Chains: A, B
Molecule details ›
Chains: A, B
Length: 241 amino acids
Theoretical weight: 25.47 KDa
Source organism: Pseudomonas aeruginosa
Expression system: Escherichia coli
UniProt:
  • Canonical: M4JT39 (Residues: 24-265; Coverage: 91%)
Gene name: blaNDM-1
Sequence domains: Metallo-beta-lactamase superfamily

Ligands and Environments

3 bound ligands:
Ligand ZN 4 x ZN
Ligand CA 4 x CA
Ligand N8Q 2 x N8Q
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X06DA
Spacegroup: P212121
Unit cell:
a: 69.678Å b: 73.665Å c: 77.501Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.185 0.207
Expression system: Escherichia coli

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Citations

4 review citations

New Carbapenemase Inhibitors: Clearing the Way for the β-Lactams.
Vázquez-Ucha et al. (2020)
3 more

2 mentions without citation

Achieving Ultrasensitive Chromogenic Probes for Rapid, Direct Detection of Carbapenemase-Producing Bacteria in Sputum.
Li et al. (2023)
1 more

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