› 1lqy

X-ray diffraction
1.9Å resolution

Crystal Structure of Bacillus stearothermophilus Peptide Deformylase Complexed with Antibiotic Actinonin

Released:
DOI: 10.2210/pdb1lqy/pdb
PDB entry 1lqy coloured by chain, front view.
PDB entry 1lqy coloured by chain, side view.
PDB entry 1lqy coloured by chain, top view.
Source organism: Geobacillus stearothermophilus
Primary publication:
The crystal structures of four peptide deformylases bound to the antibiotic actinonin reveal two distinct types: a platform for the structure-based design of antibacterial agents.
Guilloteau JP, Mathieu M, Giglione C, Blanc V, Dupuy A, Chevrier M, Gil P, Famechon A, Meinnel T, Mikol V
J Mol Biol 320 951-62 (2002)
PMID: 12126617

Function and Biology Details

Reaction catalysed: 
Formyl-L-methionyl peptide + H(2)O = formate + methionyl peptide
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-128283 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase 2 Chain: A
Molecule details ›
Chain: A
Length: 184 amino acids
Theoretical weight: 20.41 KDa
Source organism: Geobacillus stearothermophilus
Expression system: Escherichia coli
UniProt:
  • Canonical: O31410 (Residues: 1-184; Coverage: 100%)
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

2 bound ligands:
Ligand NI 2 x NI
Ligand BB2 1 x BB2
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS
Spacegroup: P212121
Unit cell:
a: 42.013Å b: 43.075Å c: 92.225Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.161 0.161 0.242
Expression system: Escherichia coli

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Citations

12 review citations

The design of inhibitors for medicinally relevant metalloproteins.
Jacobsen et al. (2007)
11 more

3 mentions without citation

Coarse-grained description of protein internal dynamics: an optimal strategy for decomposing proteins in rigid subunits.
Potestio et al. (2009)
2 more