› 2e6y

X-ray diffraction
1.6Å resolution

Covalent complex of orotidine 5'-monophosphate decarboxylase (ODCase) with 6-Iodo-UMP

Released:
DOI: 10.2210/pdb2e6y/pdb
Model geometry
Fit model/data
PDB entry 2e6y coloured by chain, front view.
PDB entry 2e6y coloured by chain, side view.
PDB entry 2e6y coloured by chain, top view.
Source organism: Methanothermobacter thermautotrophicus
Primary publication:
A potent, covalent inhibitor of orotidine 5'-monophosphate decarboxylase with antimalarial activity.
Bello AM, Poduch E, Fujihashi M, Amani M, Li Y, Crandall I, Hui R, Lee PI, Kain KC, Pai EF, Kotra LP
J Med Chem 50 915-21 (2007)
PMID: 17290979

Function and Biology Details

Reaction catalysed: 
Orotidine 5'-phosphate = UMP + CO(2)
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-127822 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Orotidine 5'-phosphate decarboxylase Chains: A, B
Molecule details ›
Chains: A, B
Length: 252 amino acids
Theoretical weight: 27.38 KDa
Source organism: Methanothermobacter thermautotrophicus
Expression system: Escherichia coli
UniProt:
  • Canonical: O26232 (Residues: 1-228; Coverage: 100%)
Gene names: MTH_129, pyrF
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

2 bound ligands:
Ligand U5P 2 x U5P
Ligand GOL 4 x GOL
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: APS BEAMLINE 14-BM-D
Spacegroup: P21
Unit cell:
a: 58.163Å b: 74.063Å c: 59.243Å
α: 90° β: 119.39° γ: 90°
R-values:
R R work R free
0.162 0.162 0.187
Expression system: Escherichia coli

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Citations

5 review citations

Purine and pyrimidine pathways as targets in Plasmodium falciparum.
Cassera et al. (2011)
4 more