Crystal structure of the PI5P4KBETA N203D-xtp complex

Structure

x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).

Ligands and binding sites

• CZC · [(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methyl phosphono hydrogen phosphate · ligand · chains A
• CZF · [[(2~{R},3~{S},4~{R},5~{R})-5-[2,6-bis(oxidanylidene)-3~{H}-purin-9-yl]-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] phosphono hydrogen phosphate · ligand · chains A

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

Pockets

11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1262 Ų buried · 19 hydrogen bonds · protein-protein

Compared structures

• 7EM7 · Crystal structure of the PI5P4Kbeta N203D-XTP complex · the same entry in another collection · chain B against B, TM-score 1.00
• P78356 · AlphaFold monomer V2.0 prediction for phosphatidylinositol 5-phosphate 4-kinase type-2… · 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 P78356
• Elsewhere: RCSB PDB 7EM7 · PDBe 7EM7 · UniProt P78356