Structure of human smoothened in complex with cholesterol and sag

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 6% strand (DSSP).

Ligands and binding sites

• V0S · 3-chloro-N-[trans-4-(methylamino)cyclohexyl]-N-{[3-(pyridin-4-yl)phenyl]methyl}-1-benzothiophene-2-carboxamide · ligand · 2 copies · chains A, B
• CLR · Cholesterol · ligand · 2 copies · chains A, B
• MPG · [(Z)-octadec-9-enyl] (2R)-2,3-bis(oxidanyl)propanoate · ligand · chains A
• NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
• NA · Sodium ion · metal · 2 copies · chains A

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 1141 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 18 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

• 7ZI0 · Structure of human Smoothened in complex with cholesterol and SAG · the same entry in another collection · chain A against A, TM-score 1.00
• Q99835 · AlphaFold monomer V2.0 prediction for smoothened homolog (Q99835) · a predicted model of the same protein · chain A against A, TM-score 0.80
• P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain B against A, TM-score 0.20

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 Q99835
• Every structure of UniProt P0ABE7
• Elsewhere: RCSB PDB 7ZI0 · PDBe 7ZI0 · UniProt Q99835 · UniProt P0ABE7