› 5a7j

X-ray diffraction
2.9Å resolution

Crystal structure of INPP5B in complex with benzene 1,2,4,5- tetrakisphosphate

Released:
DOI: 10.2210/pdb5a7j/pdb
PDB entry 5a7j coloured by chain, front view.
PDB entry 5a7j coloured by chain, side view.
PDB entry 5a7j coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase INPP5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family.
Mills SJ, Silvander C, Cozier G, Trésaugues L, Nordlund P, Potter BV
Biochemistry 55 1384-97 (2016)
PMID: 26854536

Function and Biology Details

Reaction catalysed: 
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate
Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152190 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type II inositol 1,4,5-trisphosphate 5-phosphatase Chains: A, B
Molecule details ›
Chains: A, B
Length: 313 amino acids
Theoretical weight: 36.2 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P32019 (Residues: 339-643; Coverage: 31%)
Gene names: INPP5B, OCRL2
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

3 bound ligands:
Ligand SO4 4 x SO4
Ligand K2Y 2 x K2Y
Ligand GOL 1 x GOL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P21
Unit cell:
a: 52.261Å b: 94.442Å c: 78.313Å
α: 90° β: 106.32° γ: 90°
R-values:
R R work R free
0.202 0.2 0.25
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

Targeting SHIP1 and SHIP2 in Cancer.
Pedicone et al. (2021)
8 other articles

1 mention without citation

Crystal Structures of Type-II Inositol Polyphosphate 5-Phosphatase INPP5B with Synthetic Inositol Polyphosphate Surrogates Reveal New Mechanistic Insights for the Inositol 5-Phosphatase Family.
Mills et al. (2016)