Research workbench
Structure of human smo-G111C/I496C complex with gi
Analyse Structure of human smo-G111C/I496C complex with gi in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XBK
- Type
- protein
- Length
- 1,304 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
- CLR
- Pockets
- 14 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 32% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Smoothened homolog | protein | 468 | 55% helix, 5% strand | Q99835 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 215 | 46% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 41% 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 | 5% helix, 46% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.87 | 0.90 | 73 | CLR |
| 2 | 705 | 0.80 | 0.85 | 67 | empty |
| 3 | 330 | 0.76 | 0.87 | 40 | empty |
| 4 | 713 | 0.69 | 0.76 | 59 | empty |
| 5 | 144 | 0.56 | 0.82 | 28 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2140 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1217 Ų buried · 9 hydrogen bonds · protein-protein
- R–A · 1144 Ų buried · 9 hydrogen bonds · protein-protein
- A–S · 625 Ų buried · 8 hydrogen bonds · protein-protein
- B–S · 489 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
Compared structures
- 6XBK · Structure of human SMO-G111C/I496C complex with Gi · 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
- Q99835 · AlphaFold monomer V2.0 prediction for smoothened homolog (Q99835) · a predicted model of the same protein · chain R against A, TM-score 0.94
- 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 0.93
- 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 0.82
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 6XBK · PDBe 6XBK · UniProt Q99835 · UniProt P63096 · UniProt P62873 · UniProt P59768
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