Crystal structure of active smoothened bound to SAG21K, cholesterol, and NBSMO8

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 16% strand (DSSP).

Ligands and binding sites

• OLB · (2S)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · ligand · 6 copies · chains A
• CLR · Cholesterol · ligand · 2 copies · chains A
• LKD · 3-chloro-4,7-difluoro-N-{[2-methoxy-5-(pyridin-4-yl) phenyl]methyl}-N-[trans-4-(methylamino)cyclohexyl]-1-benzothiophene-2-carboxamide · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
• NA · Sodium ion · metal · chains A
• PO4 · Phosphate ion · ion · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 1218 Ų buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

• 6O3C · Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8 · the same entry in another collection · chain A against A, TM-score 1.00
• P56726 · AlphaFold monomer V2.0 prediction for smoothened homolog (P56726) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P56726
• Elsewhere: RCSB PDB 6O3C · PDBe 6O3C · UniProt P56726