› 7pep

X-ray diffraction
1.7Å resolution

Crystal Structure of a Class D Carbapenemase Complexed with Hydrolyzed Imipenem

Released:
DOI: 10.2210/pdb7pep/pdb
PDB entry 7pep coloured by chain, front view.
PDB entry 7pep coloured by chain, side view.
PDB entry 7pep coloured by chain, top view.
Source organism: Klebsiella pneumoniae
Primary publication:
An Ion-Pair Induced Intermediate Complex Captured in Class D Carbapenemase Reveals Chloride Ion as a Janus Effector Modulating Activity
Zhou Q, Catalan P, Bell H, Baumann P, Cooke R, Evans R, Yang J, Zhang Z, Zappala D, Zhang Y, Blackburn GM, He Y, Jin Y
ACS Cent Sci (2023)

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: AAA, BBB, CCC, DDD
Molecule details ›
Chains: AAA, BBB, CCC, DDD
Length: 260 amino acids
Theoretical weight: 30.25 KDa
Source organism: Klebsiella pneumoniae
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q6XEC0 (Residues: 23-265; 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

Ligands and Environments

3 bound ligands:
Ligand HIW 4 x HIW
Ligand BR 6 x BR
Ligand 1BO 2 x 1BO
1 modified residue:
Ligand KCX 4 x KCX

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04
Spacegroup: P212121
Unit cell:
a: 83.946Å b: 107.93Å c: 124.42Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.2 0.199 0.231
Expression system: Escherichia coli BL21(DE3)

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