› 5dtt

X-ray diffraction
2.1Å resolution

Fragments bound to the OXA-48 beta-lactamase: Compound 3

Released:
DOI: 10.2210/pdb5dtt/pdb
PDB entry 5dtt coloured by chain, front view.
PDB entry 5dtt coloured by chain, side view.
PDB entry 5dtt coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
Screening and Design of Inhibitor Scaffolds for the Antibiotic Resistance Oxacillinase-48 (OXA-48) through Surface Plasmon Resonance Screening.
Lund BA, Christopeit T, Guttormsen Y, Bayer A, Leiros HK
J Med Chem 59 5542-54 (2016)
PMID: 27165692

Function and Biology Details

Reaction catalysed: 
A beta-lactam + H(2)O = a substituted beta-amino acid
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180526 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Beta-lactamase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 244 amino acids
Theoretical weight: 28.3 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6XEC0 (Residues: 22-265; Coverage: 100%)
Gene names: KPE71T_00045, bla OXA-48, blaOXA-48
Sequence domains: Penicillin binding protein transpeptidase domain
Structure domains: DD-peptidase/beta-lactamase superfamily

Ligands and Environments

3 bound ligands:
Ligand CL 2 x CL
Ligand 5F5 2 x 5F5
Ligand EDO 1 x EDO
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.2
Spacegroup: P212121
Unit cell:
a: 88.371Å b: 107.622Å c: 124.553Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.203 0.201 0.246
Expression system: Escherichia coli

Quick links

Citations

1 review citation

A review on the mechanistic details of OXA enzymes of ESKAPE pathogens.
Avci et al. (2023)
11 other articles