› 5a7i

X-ray diffraction
2.89Å resolution

Crystal structure of INPP5B in complex with biphenyl 3,3',4,4',5,5'- hexakisphosphate

Released:
DOI: 10.2210/pdb5a7i/pdb
PDB entry 5a7i coloured by chain, front view.
PDB entry 5a7i coloured by chain, side view.
PDB entry 5a7i 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
OpenAccess logo 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-542610 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Type II inositol 1,4,5-trisphosphate 5-phosphatase Chain: A
Molecule details ›
Chain: A
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
Sequence domains: Endonuclease/Exonuclease/phosphatase family 2
Structure domains: Endonuclease/exonuclease/phosphatase

Ligands and Environments

5 bound ligands:
Ligand GOL 1 x GOL
Ligand B6K 1 x B6K
Ligand PO4 3 x PO4
Ligand MG 1 x MG
Ligand CL 1 x CL
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: BESSY BEAMLINE 14.1
Spacegroup: P41212
Unit cell:
a: 96.975Å b: 96.975Å c: 152.142Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.197 0.223
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

1 review citation

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

2 mentions without citation

Structural basis for interdomain communication in SHIP2 providing high phosphatase activity.
Le Coq et al. (2017)
1 more