› 3bar

X-ray diffraction
1.9Å resolution

Crystal structure of Plasmodium falciparum orotidine 5'-phosphate decarboxylase covalently modified by 6-azido-UMP

Released:
DOI: 10.2210/pdb3bar/pdb
PDB entry 3bar coloured by chain, front view.
PDB entry 3bar coloured by chain, side view.
PDB entry 3bar coloured by chain, top view.
Source organism: Plasmodium falciparum 3D7
Primary publication:
Structure-activity relationships of C6-uridine derivatives targeting plasmodia orotidine monophosphate decarboxylase.
Bello AM, Poduch E, Liu Y, Wei L, Crandall I, Wang X, Dyanand C, Kain KC, Pai EF, Kotra LP
J Med Chem 51 439-48 (2008)
PMID: 18189347

Function and Biology Details

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

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
Molecule details ›
Chains: A, B
Length: 342 amino acids
Theoretical weight: 39.9 KDa
Source organism: Plasmodium falciparum 3D7
Expression system: Escherichia coli
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

1 bound ligand:
Ligand U5P 2 x U5P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: P21212
Unit cell:
a: 80.928Å b: 83.354Å c: 89.872Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.174 0.172 0.219
Expression system: Escherichia coli

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Citations

3 review citations

Plasmodium dihydroorotate dehydrogenase: a promising target for novel anti-malarial chemotherapy.
Phillips et al. (2010)
2 more

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)