› 3g3d

X-ray diffraction
1.7Å resolution

Crystal Structure of Human Orotidine 5'-monophosphate Decarboxylase Covalently Modified by 5-fluoro-6-azido-UMP

Released:
DOI: 10.2210/pdb3g3d/pdb
PDB entry 3g3d coloured by chain, front view.
PDB entry 3g3d coloured by chain, side view.
PDB entry 3g3d coloured by chain, top view.
Source organism: Homo sapiens
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

Reactions catalysed: 
Orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate
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-145693 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Uridine 5'-monophosphate synthase Chains: A, B
Molecule details ›
Chains: A, B
Length: 312 amino acids
Theoretical weight: 34.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11172 (Residues: 190-480; Coverage: 61%)
Gene names: OK/SW-cl.21, UMPS
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

3 bound ligands:
Ligand 5FU 2 x 5FU
Ligand GOL 3 x GOL
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: NSLS BEAMLINE X12B
Spacegroup: P21
Unit cell:
a: 69.682Å b: 61.85Å c: 70.32Å
α: 90° β: 112.73° γ: 90°
R-values:
R R work R free
0.177 0.175 0.21
Expression system: Escherichia coli

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Citations

2 review citations

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)
1 more

1 mention without citation

The Leishmania donovani UMP synthase is essential for promastigote viability and has an unusual tetrameric structure that exhibits substrate-controlled oligomerization.
French et al. (2011)