› 3s9y

X-ray diffraction
1.7Å resolution

Crystal Structure of P. falciparum orotidine 5'-monophosphate decarboxylase complexed with 5-fluoro-6-amino-UMP in space group P21, produced from 5-fluoro-6-azido-UMP

Released:
DOI: 10.2210/pdb3s9y/pdb
PDB entry 3s9y coloured by chain, front view.
PDB entry 3s9y coloured by chain, side view.
PDB entry 3s9y coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Structure-activity relationships of orotidine-5'-monophosphate decarboxylase inhibitors as anticancer agents.
Bello AM, Konforte D, Poduch E, Furlonger C, Wei L, Liu Y, Lewis M, Pai EF, Paige CJ, Kotra LP
J Med Chem 52 1648-58 (2009)
PMID: 19260677

Function and Biology Details

Reaction catalysed: 
Orotidine 5'-phosphate = UMP + CO(2)
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-184798 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
orotidine-5'-phosphate decarboxylase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 342 amino acids
Theoretical weight: 39.9 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q8IJH3 (Residues: 1-323; Coverage: 100%)
Gene name: PF3D7_1023200
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

5 bound ligands:
Ligand FNU 4 x FNU
Ligand SO4 1 x SO4
Ligand PGE 1 x PGE
Ligand PEG 1 x PEG
Ligand P6G 2 x P6G
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: APS BEAMLINE 14-BM-C
Spacegroup: P21
Unit cell:
a: 85.592Å b: 82.905Å c: 91.73Å
α: 90° β: 90.93° γ: 90°
R-values:
R R work R free
0.165 0.163 0.201
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Design of inhibitors of ODCase.
Mundra et al. (2014)
10 other articles

1 mention 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)