MolNFT v1 · #125382 · protein
Structure of human smoothened in complex with cholesterol
5L7D · Smoothened HOMOLOG,SOLUBLE cytochrome B562,SMOOTHENED…: “Structure of human smoothened in complex with cholesterol”. X-ray diffraction, 3 ligands (CLR, NAG, NA), 17 pockets (best druggability 0.82). MolNFT v1 #125382 on GenesisL1…
- PDB
- 5L7D
- Type
- protein
- Length
- 1,166 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smoothened HOMOLOG,SOLUBLE cytochrome B562,SMOOTHENED homolog
- UniProt
- Q99835, P0ABE7
- Ligands
- CLR, NAG, NA
- Pockets
- 17 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 65% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Smoothened HOMOLOG,SOLUBLE cytochrome B562,SMOOTHENED homolog | protein | 588 | 65% helix, 6% strand | Q99835, P0ABE7 |
| B | Smoothened HOMOLOG,SOLUBLE cytochrome B562,SMOOTHENED homolog | protein | 578 | 65% helix, 6% strand | Q99835, P0ABE7 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, B
- NA · Sodium ion · metal · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 443 | 0.82 | 0.90 | 57 | empty |
| 2 | 551 | 0.80 | 0.86 | 62 | empty |
| 3 | 1072 | 0.79 | 0.80 | 76 | empty |
| 4 | 78 | 0.76 | 0.98 | 27 | empty |
| 5 | 888 | 0.75 | 0.78 | 71 | NAG, CLR |
Interfaces
1 interface between chains.
- A–B · 1200 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5L7D · Structure of human Smoothened in complex with cholesterol · 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 5L7D · PDBe 5L7D · UniProt Q99835 · UniProt P0ABE7
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