› 3zcz

X-ray diffraction
2.6Å resolution

Crystal structure of a complex between Actinomadura R39 DD-peptidase and a trifluoroketone inhibitor

Released:
DOI: 10.2210/pdb3zcz/pdb
PDB entry 3zcz coloured by chain, front view.
PDB entry 3zcz coloured by chain, side view.
PDB entry 3zcz coloured by chain, top view.
Source organism: Actinomadura sp. R39
Primary publication:
Inhibition of DD-peptidases by a specific trifluoroketone: crystal structure of a complex with the Actinomadura R39 DD-peptidase.
Dzhekieva L, Adediran SA, Herman R, Kerff F, Duez C, Charlier P, Sauvage E, Pratt RF
Biochemistry 52 2128-38 (2013)
PMID: 23484909

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-153809 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 467 amino acids
Theoretical weight: 47.7 KDa
Source organism: Actinomadura sp. R39
UniProt:
  • Canonical: P39045 (Residues: 50-516; Coverage: 96%)
Gene name: dac
Sequence domains: D-Ala-D-Ala carboxypeptidase 3 (S13) family
Structure domains:

Ligands and Environments

3 bound ligands:
Ligand TFR 4 x TFR
Ligand SO4 18 x SO4
Ligand MG 4 x MG
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P21
Unit cell:
a: 103.653Å b: 91.727Å c: 106.882Å
α: 90° β: 94.3° γ: 90°
R-values:
R R work R free
0.195 0.193 0.237

Quick links

Citations

2 review citations

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

1 mention without citation

Inhibition of DD-peptidases by a specific trifluoroketone: crystal structure of a complex with the Actinomadura R39 DD-peptidase.
Dzhekieva et al. (2013)