› 2yvp

X-ray diffraction
1.66Å resolution

Crystal structure of NDX2 in complex with MG2+ and ampcpr from thermus thermophilus HB8

Released:
DOI: 10.2210/pdb2yvp/pdb
PDB entry 2yvp coloured by chain, front view.
PDB entry 2yvp coloured by chain, side view.
PDB entry 2yvp coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Primary publication:
Structural basis for different substrate specificities of two ADP-ribose pyrophosphatases from Thermus thermophilus HB8.
Wakamatsu T, Nakagawa N, Kuramitsu S, Masui R
J Bacteriol 190 1108-17 (2008)
PMID: 18039767

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
homo dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-178050 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase domain-containing protein Chain: A
Molecule details ›
Chain: A
Length: 182 amino acids
Theoretical weight: 20.34 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q5SJY9 (Residues: 1-182; Coverage: 100%)
Gene name: TTHA0863
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

2 bound ligands:
Ligand MG 3 x MG
Ligand RBY 1 x RBY
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL44B2
Spacegroup: C2221
Unit cell:
a: 40.679Å b: 100.748Å c: 97.369Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.188 0.188 0.204
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

10 citation in other articles

Structural and dynamic features of the MutT protein in the recognition of nucleotides with the mutagenic 8-oxoguanine base.
Nakamura et al. (2010)
9 more

2 mentions without citation

The evolution of function within the Nudix homology clan.
Srouji et al. (2017)
1 more