MolNFT v1 · #159545 · protein
Structure of human smoothened-gi complex
6OT0 · Smoothened homolog: “Structure of human smoothened-gi complex”. Electron microscopy, 1 ligand (CO1), 20 pockets (best druggability 0.88). MolNFT v1 #159545 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6OT0
- Type
- protein
- Length
- 1,345 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Smoothened homolog; Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine…
- UniProt
- Q99835, P63096, P62873, P59768
- Ligands
- CO1
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 6 distinct chains · 32% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Smoothened homolog | protein | 364 | 56% helix, 3% strand | Q99835 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 354 | 48% helix, 9% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 41% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 50% helix, 0% strand | P59768 |
| L | Fab light chain | protein | 104 | 0% helix, 42% strand | — |
| H | Fab heavy chain | protein | 126 | 2% helix, 42% strand | — |
Ligands and binding sites
- CO1 · 17-[3-(3,3-dimethyl-oxiranyl)-1-methyl-propyl]-10,13-dimethyl-2,3,4,7,8,9,10,11,12,13,14,15,16,17-tetradecahydro-1H-cyclopenta[a]phenanthren-3-ol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1120 | 0.88 | 0.89 | 99 | CO1 |
| 2 | 1072 | 0.84 | 0.85 | 102 | empty |
| 3 | 127 | 0.77 | 0.95 | 25 | empty |
| 4 | 588 | 0.77 | 0.84 | 78 | empty |
| 5 | 378 | 0.76 | 0.86 | 51 | empty |
Interfaces
9 interfaces between chains.
- B–G · 2009 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1501 Ų buried · 7 hydrogen bonds · protein-protein
- R–A · 1002 Ų buried · 3 hydrogen bonds · protein-protein
- L–H · 997 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 523 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6OT0 · Structure of human Smoothened-Gi complex · the same entry in another collection · chain H against H, TM-score 1.00
- P62873 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(T)… · a predicted model of the same protein · chain B against A, TM-score 0.98
- Q99835 · AlphaFold monomer V2.0 prediction for smoothened homolog (Q99835) · a predicted model of the same protein · chain R against A, TM-score 0.88
- P59768 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I)/G(S)/G(O)… · a predicted model of the same protein · chain G against A, TM-score 0.83
- P63096 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(I) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.55
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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6OT0 · PDBe 6OT0 · UniProt Q99835 · UniProt P63096 · UniProt P62873 · UniProt P59768
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