› 7ker

X-ray diffraction
1.93Å resolution

avibactam-CDD-1 45 minute complex

Released:
DOI: 10.2210/pdb7ker/pdb
PDB entry 7ker coloured by chain, front view.
PDB entry 7ker coloured by chain, side view.
PDB entry 7ker coloured by chain, top view.
Source organism: Clostridioides difficile
Primary publication:
Inhibition of the Clostridioides difficile Class D β-Lactamase CDD-1 by Avibactam.
Stewart NK, Toth M, Stasyuk A, Lee M, Smith CA, Vakulenko SB
ACS Infect Dis 7 1164-1176 (2021)
PMID: 33390002

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-168358 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-lactamase Chain: A
Molecule details ›
Chain: A
Length: 312 amino acids
Theoretical weight: 36.04 KDa
Source organism: Clostridioides difficile
Expression system: Escherichia coli

Ligands and Environments

5 bound ligands:
Ligand NXL 1 x NXL
Ligand FYG 1 x FYG
Ligand EPE 1 x EPE
Ligand SO4 5 x SO4
Ligand MPD 1 x MPD
1 modified residue:
Ligand KCX 1 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRL BEAMLINE BL12-2
Spacegroup: P4332
Unit cell:
a: 124.184Å b: 124.184Å c: 124.184Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.172 0.171 0.196
Expression system: Escherichia coli

Quick links

Citations

1 citations in other articles

In Crystallo Time-Resolved Interaction of the Clostridioides difficile CDD-1 enzyme with Avibactam Provides New Insights into the Catalytic Mechanism of Class D β-lactamases.
Stewart et al. (2021)

1 mention without citation

Inhibition of the Clostridioides difficile Class D β-Lactamase CDD-1 by Avibactam.
Stewart et al. (2021)