› 3ex4

X-ray diffraction
1.24Å resolution

human orotidyl-5'-monophosphate decarboxylase in complex with BMP

Released:
DOI: 10.2210/pdb3ex4/pdb
PDB entry 3ex4 coloured by chain, front view.
PDB entry 3ex4 coloured by chain, side view.
PDB entry 3ex4 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Lys314 is a nucleophile in non-classical reactions of orotidine-5'-monophosphate decarboxylase.
Heinrich D, Diederichsen U, Rudolph MG
Chemistry 15 6619-25 (2009)
PMID: 19472232

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: 260 amino acids
Theoretical weight: 28.3 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11172 (Residues: 224-480; 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 BMP 1 x BMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: C2221
Unit cell:
a: 77.32Å b: 116.9Å c: 62.06Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.119 0.119 0.135
Expression system: Escherichia coli

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Citations

1 review citation

Specificity in transition state binding: the Pauling model revisited.
Amyes et al. (2013)
9 other articles