› 5qjm

X-ray diffraction
1.75Å resolution

PanDDA analysis group deposition of models with modelled events (e.g. bound ligands) -- Crystal Structure of NUDT5 in complex with Z328695024

Released:
DOI: 10.2210/pdb5qjm/pdb
PDB entry 5qjm coloured by chain, front view.
PDB entry 5qjm coloured by chain, side view.
PDB entry 5qjm coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Dubianok Y, Collins P, Krojer T, Wright N, Strain-Damerell C, Burgess-Brown N, Bountra C, Arrowsmith CH, Edwards A, Huber K, von Delft F

Function and Biology Details

Reactions catalysed: 
ATP + D-ribose 5-phosphate = diphosphate + ADP-D-ribose
ADP-D-ribose + H(2)O = AMP + D-ribose 5-phosphate
8-oxo-GDP + H(2)O = 8-oxo-GMP + phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-193850 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
ADP-sugar pyrophosphatase Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 209 amino acids
Theoretical weight: 23.14 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9UKK9 (Residues: 1-208; Coverage: 95%)
Gene names: HSPC115, NUDIX5, NUDT5
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

4 bound ligands:
Ligand MG 8 x MG
Ligand K1G 4 x K1G
Ligand CL 1 x CL
Ligand EDO 3 x EDO
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P1
Unit cell:
a: 49.637Å b: 59.95Å c: 80.267Å
α: 79.09° β: 81.28° γ: 75.44°
R-values:
R R work R free
0.225 0.222 0.271
Expression system: Escherichia coli

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