› 5dtk

X-ray diffraction
1.6Å resolution

Fragments bound to the OXA-48 beta-lactamase: Compound 17

Released:
DOI: 10.2210/pdb5dtk/pdb
PDB entry 5dtk coloured by chain, front view.
PDB entry 5dtk coloured by chain, side view.
PDB entry 5dtk 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: 265 amino acids
Theoretical weight: 30.44 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli
UniProt:
  • Canonical: Q6XEC0 (Residues: 1-265; Coverage: 100%)
Gene names: AI2879V1_5232, GJJ21_26815, KPE71T_00045, SAMEA3727706_05517, bla OXA-48, blaOXA-48, bla_4
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 EDO 13 x EDO
Ligand 5F3 4 x 5F3
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 45.523Å b: 124.31Å c: 108.742Å
α: 90° β: 98.263° γ: 90°
R-values:
R R work R free
0.146 0.146 0.172
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)
9 other articles

3 mentions without citation

Structure, activity and thermostability investigations of OXA-163, OXA-181 and OXA-245 using biochemical analysis, crystal structures and differential scanning calorimetry analysis.
Lund et al. (2017)
2 more