Crystal structure of XWNT8 in complex with the cysteine-rich domain of frizzled 8

Structure

x-ray diffraction · 2 distinct chains · 42% helix, 14% strand (DSSP).

Ligands and binding sites

• PAM · Palmitoleic acid · ligand · chains A, B
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
• BMA · beta-D-mannopyranose · sugar · 2 copies
• MAN · alpha-D-mannopyranose · sugar
• FUC · alpha-L-fucopyranose · sugar · chains B
• ZN · Zinc ion · metal · 3 copies · chains B

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 747 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 16 disulfide, 3 glycan, 1 covalent (disulfide, N-glycosylation, covalent ligand).

Compared structures

• 4F0A · Crystal structure of XWnt8 in complex with the cysteine-rich domain of Frizzled 8 · the same entry in another collection · chain A against A, TM-score 1.00
• Q61091 · AlphaFold monomer V2.0 prediction for frizzled-8 (Q61091) · a predicted model of the same protein · chain A against A, TM-score 0.97
• P28026 · AlphaFold monomer V2.0 prediction for protein wnt-8 (P28026) · a predicted model of the same protein · chain B against A, TM-score 0.94

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 Q61091
• Every structure of UniProt P28026
• Elsewhere: RCSB PDB 4F0A · PDBe 4F0A · UniProt Q61091 · UniProt P28026