› 4kqr

X-ray diffraction
2.01Å resolution

CRYSTAL STRUCTURE OF PENICILLIN-BINDING PROTEIN 3 FROM PSEUDOMONAS AERUGINOSA IN COMPLEX WITH (5S)-Penicilloic Acid

Released:
DOI: 10.2210/pdb4kqr/pdb
PDB entry 4kqr coloured by chain, front view.
PDB entry 4kqr coloured by chain, side view.
PDB entry 4kqr coloured by chain, top view.
Source organism: Pseudomonas aeruginosa PAO1
Primary publication:
Binding of (5S)-penicilloic acid to penicillin binding protein 3.
van Berkel SS, Nettleship JE, Leung IK, Brem J, Choi H, Stuart DI, Claridge TD, McDonough MA, Owens RJ, Ren J, Schofield CJ
ACS Chem Biol 8 2112-6 (2013)
PMID: 23899657

Function and Biology Details

Reaction catalysed: 
Preferential cleavage: (Ac)(2)-L-Lys-D-Ala-|-D-Ala. Also transpeptidation of peptidyl-alanyl moieties that are N-acyl substituents of D-alanine.
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-124404 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptidoglycan D,D-transpeptidase FtsI Chains: A, B
Molecule details ›
Chains: A, B
Length: 564 amino acids
Theoretical weight: 61.15 KDa
Source organism: Pseudomonas aeruginosa PAO1
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: G3XD46 (Residues: 35-579; Coverage: 94%)
Gene names: PA4418, ftsI, pbpB
Sequence domains:
Structure domains: DD-peptidase/beta-lactamase superfamily

Ligands and Environments

4 bound ligands:
Ligand VPP 2 x VPP
Ligand CL 5 x CL
Ligand GOL 9 x GOL
Ligand IMD 3 x IMD
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I24
Spacegroup: P1
Unit cell:
a: 57.199Å b: 75.453Å c: 83.218Å
α: 70.77° β: 85.4° γ: 85.06°
R-values:
R R work R free
0.186 0.185 0.207
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

4 review citations

Glycosyltransferases and Transpeptidases/Penicillin-Binding Proteins: Valuable Targets for New Antibacterials.
Sauvage et al. (2016)
3 more

2 mentions without citation

Crystal structures of penicillin-binding protein 3 in complexes with azlocillin and cefoperazone in both acylated and deacylated forms.
Ren et al. (2016)
1 more