› 2xk1

X-ray diffraction
2.8Å resolution

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

Released:
DOI: 10.2210/pdb2xk1/pdb
PDB entry 2xk1 coloured by chain, front view.
PDB entry 2xk1 coloured by chain, side view.
PDB entry 2xk1 coloured by chain, top view.
Source organism: Actinomadura sp. R39
Primary publication:
Structure guided development of potent reversibly binding penicillin binding protein inhibitors.
Woon EC, Zervosen A, Sauvage E, Simmons KJ, Zivec M, Inglis SR, Fishwick CW, Gobec S, Charlier P, Luxen A, Schofield CJ
ACS Med Chem Lett 2 219-23 (2011)
PMID: 24900305

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: 466 amino acids
Theoretical weight: 47.65 KDa
Source organism: Actinomadura sp. R39
UniProt:
  • 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:
Ligand EWB 4 x EWB
Ligand SO4 16 x SO4
Ligand CO 4 x CO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE BM30A
Spacegroup: C2
Unit cell:
a: 154.898Å b: 92.348Å c: 143.829Å
α: 90° β: 92.25° γ: 90°
R-values:
R R work R free
0.219 0.217 0.264

Quick links

Citations

4 review citations

Development of new drugs for an old target: the penicillin binding proteins.
Zervosen et al. (2012)
3 more

1 mention without citation

Structure guided development of potent reversibly binding penicillin binding protein inhibitors.
Woon et al. (2011)