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X-ray diffraction
2.8Å resolution

Crystals of Peptide Deformylase from Plasmodium falciparum with Ten Subunits per Asymmetric Unit Reveal Critical Characteristics of the Active Site for Drug Design

Released:
DOI: 10.2210/pdb1jym/pdb
PDB entry 1jym coloured by chain, front view.
PDB entry 1jym coloured by chain, side view.
PDB entry 1jym coloured by chain, top view.
Source organism: Plasmodium falciparum
Primary publication:
Crystals of peptide deformylase from Plasmodium falciparum reveal critical characteristics of the active site for drug design.
Kumar A, Nguyen KT, Srivathsan S, Ornstein B, Turley S, Hirsh I, Pei D, Hol WG
Structure 10 357-67 (2002)
PMID: 12005434

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 domain:

Structure analysis Details

Assembly composition:
homo decamer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184654 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Peptide deformylase Chains: A, B, C, D, E, F, G, H, I, J
Molecule details ›
Chains: A, B, C, D, E, F, G, H, I, J
Length: 183 amino acids
Theoretical weight: 21.82 KDa
Source organism: Plasmodium falciparum
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8I372 (Residues: 63-239; Coverage: 73%)
Gene name: PF3D7_0907900
Sequence domains: Polypeptide deformylase
Structure domains: Peptide deformylase

Ligands and Environments

1 bound ligand:
Ligand CO 10 x CO
1 modified residue:
Ligand MSE 30 x MSE

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 5.0.2
Spacegroup: P41
Unit cell:
a: 121.263Å b: 121.263Å c: 177.272Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.234 0.231 0.296
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

5 review citations

Mitochondrial evolution and functions in malaria parasites.
Vaidya et al. (2009)
4 more

4 mentions without citation

The Potential of Secondary Metabolites from Plants as Drugs or Leads against Protozoan Neglected Diseases-Part III: In-Silico Molecular Docking Investigations.
Ogungbe et al. (2016)
3 more