Research workbench
Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8
Analyse Crystal structure of active Smoothened bound to SAG21k, cholesterol, and NbSmo8 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6O3C
- Type
- protein
- Length
- 606 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Mus musculus; SYNTHETIC CONSTRUCT
- Molecule
- Smoothened homolog; NbSmo8
- UniProt
- P56726
- Ligands
- OLB, CLR, LKD, NAG, NA, PO4
- Pockets
- 7 · best druggability 0.88
Structure
x-ray diffraction · resolution 2.8 · 2 distinct chains · 48% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smoothened homolog | protein | 484 | 60% helix, 7% strand | P56726 |
| B | NbSmo8 | protein | 122 | 2% helix, 51% strand | — |
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.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 803 | 0.88 | 0.91 | 70 | LKD, CLR |
| 2 | 342 | 0.67 | 0.81 | 34 | CLR |
| 3 | 158 | 0.50 | 0.78 | 24 | empty |
| 4 | 58 | 0.49 | 0.86 | 17 | empty |
| 5 | 136 | 0.41 | 0.74 | 22 | empty |
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
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