› 7oqf

X-ray diffraction
1.05Å resolution

Human OMPD-domain of UMPS in complex with OMP at 1.05 Angstrom resolution, 5 minutes soaking

Released:
DOI: 10.2210/pdb7oqf/pdb
PDB entry 7oqf coloured by chain, front view.
PDB entry 7oqf coloured by chain, side view.
PDB entry 7oqf 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:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145692 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Uridine 5'-monophosphate synthase Chain: A
Molecule details ›
Chain: A
Length: 257 amino acids
Theoretical weight: 28.11 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P11172 (Residues: 224-480; Coverage: 54%)
Gene names: OK/SW-cl.21, UMPS
Sequence domains: Orotidine 5'-phosphate decarboxylase / HUMPS family
Uridine 5'-monophosphate synthase Chain: B
Molecule details ›
Chain: B
Length: 257 amino acids
Theoretical weight: 28.08 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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 GOL 2 x GOL
Ligand SO4 4 x SO4
Ligand OMP 2 x OMP
Ligand U 2 x U
2 modified residues:
Ligand CSS 1 x CSS
Ligand ALY 2 x ALY

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: P21
Unit cell:
a: 70.097Å b: 61.97Å c: 70.09Å
α: 90° β: 113° γ: 90°
R-values:
R R work R free
0.138 0.137 0.153
Expression system: Escherichia coli BL21(DE3)

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