Structure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumination at 405 nm and 180 K

Structure

x-ray diffraction · 2 distinct chains · 0% helix, 50% strand (DSSP).

Ligands and binding sites

• ALQ · 2-methyl-propionic acid · ligand · chains A, B
• 4FO · (2R)-2,4-diaminobutanoic acid · ligand · chains A, B
• EDN · Ethane-1,2-diamine · ligand · chains B
• S7Z · (E)-(4-((2,6-difluoro-4-(hydroxymethyl)phenyl) diazenyl)-2,6-difluorophenyl)methanol · ligand · chains A, B

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

Pockets

3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 360 Ų buried · 4 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 2 covalent, 1 d-amino, 1 modified (covalent ligand, D-amino acid, nonstandard).

Compared structures

• 7AXQ · Structure of the cryo-trapped WDR5:CS-VIP8 cocrystal after illumination at 405 nm and 180… · the same entry in another collection · chain A against A, TM-score 1.00
• P61964 · AlphaFold monomer V2.0 prediction for wd repeat-containing protein 5 (P61964) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 P61964
• Elsewhere: RCSB PDB 7AXQ · PDBe 7AXQ · UniProt P61964