› 3g3m

X-ray diffraction
1.4Å resolution

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

Released:
DOI: 10.2210/pdb3g3m/pdb
PDB entry 3g3m coloured by chain, front view.
PDB entry 3g3m coloured by chain, side view.
PDB entry 3g3m 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 Chain: A
Molecule details ›
Chain: A
Length: 279 amino acids
Theoretical weight: 30.49 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11172 (Residues: 223-480; Coverage: 54%)
Gene names: OK/SW-cl.21, UMPS
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Structure domains: Aldolase class I

Ligands and Environments

1 bound ligand:
Ligand 5FU 1 x 5FU
1 modified residue:
Ligand CSX 1 x CSX

Experiments and Validation Details

Entry percentile scores
X-ray source: CLSI BEAMLINE 08ID-1
Spacegroup: C2221
Unit cell:
a: 78.28Å b: 116.558Å c: 62.113Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.16 0.159 0.182
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 structure of the catechin-binding site of human sulfotransferase 1A1.
Cook et al. (2016)