› 5rx1

X-ray diffraction
1.31Å resolution

INPP5D PanDDA analysis group deposition -- Crystal Structure of the phosphatase and C2 domains of SHIP1 in complex with Z2466069494

Released:
DOI: 10.2210/pdb5rx1/pdb
PDB entry 5rx1 coloured by chain, front view.
PDB entry 5rx1 coloured by chain, side view.
PDB entry 5rx1 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Regulation of inositol 5-phosphatase activity by the C2 domain of SHIP1 and SHIP2.
Bradshaw WJ, Kennedy EC, Moreira T, Smith LA, Chalk R, Katis VL, Benesch JLP, Brennan PE, Murphy EJ, Gileadi O
Structure (2024)
PMID: 38309262

Function and Biology Details

Reactions catalysed: 
1-phosphatidyl-1D-myo-inositol 4,5-bisphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 4-phosphate + phosphate
1D-myo-inositol 1,3,4,5-tetrakisphosphate + H(2)O = 1D-myo-inositol 1,3,4-trisphosphate + phosphate
1-phosphatidyl-1D-myo-inositol 3,4,5-triphosphate + H(2)O = 1-phosphatidyl-1D-myo-inositol 3,4-diphosphate + 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-187774 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Phosphatidylinositol 3,4,5-trisphosphate 5-phosphatase 1 Chain: A
Molecule details ›
Chain: A
Length: 463 amino acids
Theoretical weight: 52.88 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q92835 (Residues: 397-857; Coverage: 39%)
Gene names: INPP5D, SHIP, SHIP1
Sequence domains: Endonuclease/Exonuclease/phosphatase family 2

Ligands and Environments

3 bound ligands:
Ligand WMG 1 x WMG
Ligand WMD 1 x WMD
Ligand DMS 3 x DMS
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: DIAMOND BEAMLINE I04-1
Spacegroup: P212121
Unit cell:
a: 62.67Å b: 79.21Å c: 89.5Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.176 0.175 0.197
Expression system: Spodoptera frugiperda

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