› 3ex6

X-ray diffraction
1.3Å resolution

D312N mutant of human orotidyl-5'-monophosphate decarboxylase in complex with 6-azido-UMP, covalent adduct

Released:
DOI: 10.2210/pdb3ex6/pdb
PDB entry 3ex6 coloured by chain, front view.
PDB entry 3ex6 coloured by chain, side view.
PDB entry 3ex6 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 Chains: A, B
Molecule details ›
Chains: A, B
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

4 bound ligands:
Ligand GOL 1 x GOL
Ligand SO4 2 x SO4
Ligand CL 1 x CL
Ligand U5P 1 x U5P
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P21
Unit cell:
a: 69.49Å b: 61.58Å c: 70.72Å
α: 90° β: 113.43° γ: 90°
R-values:
R R work R free
0.169 0.167 0.197
Expression system: Escherichia coli

Quick links

Citations

1 review citation

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