› 6yvm

X-ray diffraction
1.25Å resolution

Human OMPD-domain of UMPS in complex with the substrate OMP at 1.25 Angstroms resolution, 2.13 MGy exposure

Released:
DOI: 10.2210/pdb6yvm/pdb
PDB entry 6yvm coloured by chain, front view.
PDB entry 6yvm coloured by chain, side view.
PDB entry 6yvm coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Ground-state destabilization by electrostatic repulsion is not a driving force in orotidine-5-monophosphate decarboxylase catalysis
Rindfleisch S, Krull M, Uranga J, Schmidt T, Rabe von Pappenheim F, Kirck LL, Balouri A, Schneider T, Chari A, Kluger R, Bourenkov G, Diederichsen U, Mata RA, Tittmann K
Nat Catal 5 332-341 (2022)

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: 28.37 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

Ligands and Environments

4 bound ligands:
Ligand OMP 1 x OMP
Ligand U 1 x U
Ligand GOL 1 x GOL
Ligand SO4 6 x SO4
2 modified residues:
Ligand CSS 1 x CSS
Ligand ALY 1 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: C2221
Unit cell:
a: 77.33Å b: 116.86Å c: 61.98Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.133 0.131 0.158
Expression system: Escherichia coli

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