› 3i7u

X-ray diffraction
1.8Å resolution

Crystal structure of AP4A hydrolase (aq_158) from Aquifex aeolicus VF5

Released:
DOI: 10.2210/pdb3i7u/pdb
PDB entry 3i7u coloured by chain, front view.
PDB entry 3i7u coloured by chain, side view.
PDB entry 3i7u coloured by chain, top view.
Source organism: Aquifex aeolicus VF5
Primary publication:
Free and ATP-bound structures of Ap4A hydrolase from Aquifex aeolicus V5.
Jeyakanthan J, Kanaujia SP, Nishida Y, Nakagawa N, Praveen S, Shinkai A, Kuramitsu S, Yokoyama S, Sekar K
Acta Crystallogr D Biol Crystallogr 66 116-24 (2010)
PMID: 20124691

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
homo tetramer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-130339 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Nudix hydrolase domain-containing protein Chains: A, B, C, D
Molecule details ›
Chains: A, B, C, D
Length: 134 amino acids
Theoretical weight: 15.79 KDa
Source organism: Aquifex aeolicus VF5
Expression system: Escherichia coli
UniProt:
  • Canonical: O66548 (Residues: 1-134; Coverage: 100%)
Gene names: apfA, aq_158
Sequence domains: NUDIX domain
Structure domains: Nucleoside Triphosphate Pyrophosphohydrolase

Ligands and Environments

6 bound ligands:
Ligand CL 11 x CL
Ligand EDO 11 x EDO
Ligand PEG 4 x PEG
Ligand TRS 1 x TRS
Ligand PGE 2 x PGE
Ligand PG4 1 x PG4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL26B2
Spacegroup: P21
Unit cell:
a: 85.589Å b: 38.049Å c: 87.592Å
α: 90° β: 93.1° γ: 90°
R-values:
R R work R free
0.203 0.203 0.239
Expression system: Escherichia coli

Quick links

Citations

1 review citation

The mysterious diadenosine tetraphosphate (AP4A).
Zegarra et al. (2023)
3 other articles

1 mention without citation

Crystal structure of wild-type and mutant human Ap4A hydrolase.
Ge et al. (2013)