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› 6dsr

X-ray diffraction
2.6Å resolution

Re-refinement of P. falciparum orotidine 5'-monophosphate decarboxylase

Released:
DOI: 10.2210/pdb6dsr/pdb
Model geometry
Fit model/data
PDB entry 6dsr coloured by chain, front view.
PDB entry 6dsr coloured by chain, side view.
PDB entry 6dsr coloured by chain, top view.
Source organism: Plasmodium falciparum
Primary publication:
Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target.
Novak WRP, West KHJ, Kirkman LMD, Brandt GS
Acta Crystallogr F Struct Biol Commun 74 664-668 (2018)
PMID: 30279319

Function and Biology Details

Reaction catalysed: 
orotidine 5'-phosphate + H(+) = UMP + CO2.
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-186132 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Orotidine 5'-phosphate decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 323 amino acids
Theoretical weight: 37.87 KDa
Source organism: Plasmodium falciparum
Expression system: Escherichia coli
UniProt:
  • Canonical: Q8T6J6 (Residues: 1-323; Coverage: 100%)
Gene name: ompdc
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

wwPDB Validation report is not available for this entry.
X-ray source: SPRING-8 BEAMLINE BL38B1
Spacegroup: R3
Unit cell:
a: 201.879Å b: 201.879Å c: 44.191Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.185 0.182 0.224
Expression system: Escherichia coli

Quick links

Citations

1 mention without citation

Re-refinement of Plasmodium falciparum orotidine 5'-monophosphate decarboxylase provides a clearer picture of an important malarial drug target.
Novak et al. (2018)