› 6zx3

X-ray diffraction
1.15Å resolution

OMPD-domain of human UMPS in complex with 6-thiocarboxamido-UMP at 1.15 Angstroms resolution

Released:
DOI: 10.2210/pdb6zx3/pdb
PDB entry 6zx3 coloured by chain, front view.
PDB entry 6zx3 coloured by chain, side view.
PDB entry 6zx3 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: 28.3 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

Ligands and Environments

4 bound ligands:
Ligand QRZ 1 x QRZ
Ligand GOL 1 x GOL
Ligand PRO 1 x PRO
Ligand SO4 1 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PETRA III, EMBL c/o DESY BEAMLINE P14 (MX2)
Spacegroup: C2221
Unit cell:
a: 77.46Å b: 116.11Å c: 62.13Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.128 0.126 0.15
Expression system: Escherichia coli

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