› 1vc9

X-ray diffraction
2.3Å resolution

Crystal Structure of a T.thermophilus HB8 Ap6A hydrolase E50Q mutant-Mg2+-ATP complex

Released:
DOI: 10.2210/pdb1vc9/pdb
PDB entry 1vc9 coloured by chain, front view.
PDB entry 1vc9 coloured by chain, side view.
PDB entry 1vc9 coloured by chain, top view.
Source organism: Thermus thermophilus HB8
Entry authors: Iwai T, Nakagawa N, Kuramitsu S, Masui R, RIKEN Structural Genomics/Proteomics Initiative (RSGI)

Function and Biology Details

Reaction catalysed: 
P(1),P(4)-bis(5'-adenosyl)tetraphosphate + H(2)O = ATP + AMP
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-181121 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Diadenosine hexaphosphate hydrolase Chains: A, B
Molecule details ›
Chains: A, B
Length: 126 amino acids
Theoretical weight: 14.19 KDa
Source organism: Thermus thermophilus HB8
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: Q75UV1 (Residues: 1-126; Coverage: 100%)
Gene name: ndx1
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

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

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P212121
Unit cell:
a: 47.9Å b: 55.121Å c: 113.869Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.216 0.216 0.252
Expression system: Escherichia coli BL21(DE3)

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