› 3o3j

X-ray diffraction
3Å resolution

Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) in complex with inhibitor 6b

Released:
DOI: 10.2210/pdb3o3j/pdb
PDB entry 3o3j coloured by chain, front view.
PDB entry 3o3j coloured by chain, side view.
PDB entry 3o3j coloured by chain, top view.
Source organism: Arabidopsis thaliana
Primary publication:
Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.
Fieulaine S, Boularot A, Artaud I, Desmadril M, Dardel F, Meinnel T, Giglione C
PLoS Biol 9 e1001066 (2011)
PMID: 21629676

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-190373 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase 1B, chloroplastic/mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 193 amino acids
Theoretical weight: 21.98 KDa
Source organism: Arabidopsis thaliana
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9FUZ2 (Residues: 83-273; Coverage: 70%)
Gene names: At5g14660, DEF2, PDF1B, T15N1_150
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

2 bound ligands:
Ligand ZN 6 x ZN
Ligand BB4 1 x BB4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SOLEIL BEAMLINE PROXIMA 1
Spacegroup: P43212
Unit cell:
a: 57.5Å b: 57.5Å c: 144.84Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.209 0.2 0.285
Expression system: Escherichia coli

Quick links

Citations

21 citation in other articles

Avibactam is a covalent, reversible, non-β-lactam β-lactamase inhibitor.
Ehmann et al. (2012)
20 more

1 mention without citation

Trapping conformational states along ligand-binding dynamics of peptide deformylase: the impact of induced fit on enzyme catalysis.
Fieulaine et al. (2011)