› 1sde

X-ray diffraction
1.15Å resolution

Toward Better Antibiotics: Crystal Structure Of D-Ala-D-Ala Peptidase inhibited by a novel bicyclic phosphate inhibitor

Released:
DOI: 10.2210/pdb1sde/pdb
PDB entry 1sde coloured by chain, front view.
PDB entry 1sde coloured by chain, side view.
PDB entry 1sde coloured by chain, top view.
Source organism: Streptomyces sp. R61
Primary publication:
Toward better antibiotics: crystallographic studies of a novel class of DD-peptidase/beta-lactamase inhibitors.
Silvaggi NR, Kaur K, Adediran SA, Pratt RF, Kelly JA
Biochemistry 43 7046-53 (2004)
PMID: 15170342

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: 347 amino acids
Theoretical weight: 37.22 KDa
Source organism: Streptomyces sp. R61
UniProt:
  • Canonical: P15555 (Residues: 32-378; Coverage: 93%)
Sequence domains: Beta-lactamase
Structure domains: DD-peptidase/beta-lactamase superfamily

Ligands and Environments

2 bound ligands:
Ligand 2PB 1 x 2PB
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: P212121
Unit cell:
a: 50.8Å b: 66.7Å c: 100.1Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.119 0.101 0.14

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Citations

1 review citation

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

1 mention without citation

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