› 1v8s

X-ray diffraction
2.2Å resolution

Crystal structure analusis of the ADP-ribose pyrophosphatase complexed with AMP and Mg

Released:
DOI: 10.2210/pdb1v8s/pdb
PDB entry 1v8s coloured by chain, front view.
PDB entry 1v8s coloured by chain, side view.
PDB entry 1v8s coloured by chain, top view.
Source organism: Thermus thermophilus
Primary publication:
Structural insights into the Thermus thermophilus ADP-ribose pyrophosphatase mechanism via crystal structures with the bound substrate and metal.
Yoshiba S, Ooga T, Nakagawa N, Shibata T, Inoue Y, Yokoyama S, Kuramitsu S, Masui R
J Biol Chem 279 37163-74 (2004)
PMID: 15210687

Function and Biology Details

Reaction catalysed: 
ADP-D-ribose + H(2)O = AMP + D-ribose 5-phosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-183026 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 19.29 KDa
Source organism: Thermus thermophilus
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q84CU3 (Residues: 1-170; Coverage: 100%)
Gene name: ndx4
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand MG 1 x MG
Ligand AMP 1 x AMP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P3221
Unit cell:
a: 49.74Å b: 49.74Å c: 118.12Å
α: 90° β: 90° γ: 120°
R-values:
R R work R free
0.199 0.199 0.248
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Structures and mechanisms of Nudix hydrolases.
Mildvan et al. (2005)
19 other articles