› 1vc8

X-ray diffraction
2Å resolution

Crystal Structure of a T.thermophilus HB8 Ap6A Hydrolase Ndx1-Ap6A Complex

Released:
DOI: 10.2210/pdb1vc8/pdb
PDB entry 1vc8 coloured by chain, front view.
PDB entry 1vc8 coloured by chain, side view.
PDB entry 1vc8 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

1 bound ligand:
Ligand 5FA 2 x 5FA
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU FR-E
Spacegroup: P212121
Unit cell:
a: 52.413Å b: 54.775Å c: 111.673Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.195 0.195 0.225
Expression system: Escherichia coli BL21(DE3)

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