X-ray diffraction
2.65Å resolution

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

Source organism: Actinomadura sp. R39
Entry authors: Cannella SE, Sauvage E, Herman R, Kerff F, Rocaboy M, Charlier P

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:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
D-alanyl-D-alanine carboxypeptidase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 466 amino acids
Theoretical weight: 47.65 KDa
Source organism: Actinomadura sp. R39
  • Canonical: P39045 (Residues: 50-515; Coverage: 95%)
Gene name: dac
Sequence domains: D-Ala-D-Ala carboxypeptidase 3 (S13) family
Structure domains:

Ligands and Environments

3 bound ligands:
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: P21
Unit cell:
a: 102.332Å b: 92.113Å c: 105.957Å
α: 90° β: 95.9° γ: 90°
R R work R free
0.22 0.217 0.268