The structure of the first ywtd beta propeller domain of LRP6 in complex with a DKK1 peptide

Structure

x-ray diffraction · 2 distinct chains · 4% helix, 48% strand (DSSP).

Ligands and binding sites

• ACE · Acetyl group · ligand · chains Z
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
• FUC · alpha-L-fucopyranose · sugar · chains A
• CA · Calcium ion · metal · chains A
• NH2 · Amino group · ion · chains Z
• GOL · Glycerol · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–Z · 479 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

• 3SOQ · The structure of the first YWTD beta propeller domain of LRP6 in complex with a DKK1… · the same entry in another collection · chain A against A, TM-score 1.00
• O75581 · AlphaFold monomer V2.0 prediction for low-density lipoprotein receptor-related protein 6… · a predicted model of the same protein · chain A against A, TM-score 0.99
• O94907 · AlphaFold monomer V2.0 prediction for dickkopf-related protein 1 (O94907) · a predicted model of the same protein · chain Z against A, TM-score 0.52

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 O75581
• Every structure of UniProt O94907
• Elsewhere: RCSB PDB 3SOQ · PDBe 3SOQ · UniProt O75581 · UniProt O94907