› 1ikg

X-ray diffraction
1.9Å resolution

MICHAELIS COMPLEX OF STREPTOMYCES R61 DD-PEPTIDASE WITH A SPECIFIC PEPTIDOGLYCAN SUBSTRATE FRAGMENT

Released:
DOI: 10.2210/pdb1ikg/pdb
PDB entry 1ikg coloured by chain, front view.
PDB entry 1ikg coloured by chain, side view.
PDB entry 1ikg coloured by chain, top view.
Source organism: Streptomyces sp. R61
Primary publication:
Structures of two kinetic intermediates reveal species specificity of penicillin-binding proteins.
McDonough MA, Anderson JW, Silvaggi NR, Pratt RF, Knox JR, Kelly JA
J Mol Biol 322 111-22 (2002)
PMID: 12215418

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 domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-147403 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
D-alanyl-D-alanine carboxypeptidase Chain: A
Molecule details ›
Chain: A
Length: 349 amino acids
Theoretical weight: 37.42 KDa
Source organism: Streptomyces sp. R61
UniProt:
  • Canonical: P15555 (Residues: 32-380; Coverage: 93%)
Sequence domains: Beta-lactamase
Structure domains: DD-peptidase/beta-lactamase superfamily

Ligands and Environments

1 bound ligand:
Ligand REX 1 x REX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU RU200
Spacegroup: P212121
Unit cell:
a: 50.873Å b: 66.828Å c: 100.129Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.15 0.184

Quick links

Citations

4 review citations

The penicillin-binding proteins: structure and role in peptidoglycan biosynthesis.
Sauvage et al. (2008)
3 more

5 mentions without citation

Pharmacophore-based virtual screening versus docking-based virtual screening: a benchmark comparison against eight targets.
Chen et al. (2009)
4 more