Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate kinase 2 (PPIP5K2) in complex with ADP and 1,5- (PA)2-IP4

Structure

x-ray diffraction · 1 distinct chain · 27% helix, 32% strand (DSSP).

Ligands and binding sites

• ADP · Adenosine-5'-diphosphate · ligand · chains A
• 4WY · {[(1R,3S,4S,5R,6S)-2,4,5,6-tetrakis(phosphonooxy) cyclohexane-1,3-diyl]bis[oxy(2-oxoethane-2,1-diyl) ]}bis(phosphonic acid) · ligand · chains A
• MG · Magnesium ion · metal · 3 copies · chains A
• EDO · 1,2-ethanediol · additive · 4 copies · chains A
• ACT · Acetate ion · additive · 3 copies · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Compared structures

• 5BYB · Crystal structure of the catalytic domain of human diphosphoinositol pentakisphosphate… · the same entry in another collection · chain A against A, TM-score 1.00
• O43314 · AlphaFold monomer V2.0 prediction for inositol hexakisphosphate and… · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt O43314
• Elsewhere: RCSB PDB 5BYB · PDBe 5BYB · UniProt O43314