MolNFT v1 · #169429 · protein
Structure of human smo-gi complex with 24(S),25-ec
6XBM · Smoothened homolog: “Structure of human smo-gi complex with 24(S),25-ec”. Electron microscopy, 1 ligand (CO1), 11 pockets (best druggability 0.85). MolNFT v1 #169429 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XBM
- Type
- protein
- Length
- 1,170 residues
- Chains
- 5
- 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
- 11 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 33% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Smoothened homolog | protein | 331 | 68% helix, 4% strand | Q99835 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 215 | 47% helix, 17% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 7% helix, 44% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 53% helix, 0% strand | P59768 |
| S | SCFV16 | protein | 232 | 1% helix, 47% 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 · 2 copies · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 942 | 0.85 | 0.86 | 76 | CO1 |
| 2 | 745 | 0.82 | 0.85 | 66 | empty |
| 3 | 742 | 0.69 | 0.76 | 68 | empty |
| 4 | 287 | 0.63 | 0.81 | 59 | empty |
| 5 | 195 | 0.49 | 0.76 | 34 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2181 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1165 Ų buried · 15 hydrogen bonds · protein-protein
- R–A · 1075 Ų buried · 11 hydrogen bonds · protein-protein
- A–S · 621 Ų buried · 11 hydrogen bonds · protein-protein
- B–S · 489 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6XBM · Structure of human SMO-Gi complex with 24(S),25-EC · the same entry in another collection · chain S against S, 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 0.99
- 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 0.95
- Q99835 · AlphaFold monomer V2.0 prediction for smoothened homolog (Q99835) · a predicted model of the same protein · chain R against A, TM-score 0.93
- 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 0.81
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 6XBM · PDBe 6XBM · UniProt Q99835 · UniProt P63096 · UniProt P62873 · UniProt P59768
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.