MolNFT v1 · #169426 · protein
Structure of human smo-D384R complex with gi
6XBJ · Smoothened homolog: “Structure of human smo-D384R complex with gi”. Electron microscopy, 1 ligand (CLR), 18 pockets (best druggability 0.86). MolNFT v1 #169426 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XBJ
- Type
- protein
- Length
- 1,301 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
- 18 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 32% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Smoothened homolog | protein | 465 | 56% helix, 5% strand | Q99835 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 215 | 48% helix, 15% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 336 | 7% helix, 40% 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 | 3% helix, 43% 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
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 582 | 0.86 | 0.91 | 79 | CLR |
| 2 | 660 | 0.81 | 0.85 | 62 | empty |
| 3 | 236 | 0.74 | 0.88 | 33 | empty |
| 4 | 60 | 0.72 | 0.97 | 19 | empty |
| 5 | 898 | 0.70 | 0.75 | 75 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2145 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 1242 Ų buried · 9 hydrogen bonds · protein-protein
- R–A · 1164 Ų buried · 6 hydrogen bonds · protein-protein
- A–S · 631 Ų buried · 7 hydrogen bonds · protein-protein
- B–S · 492 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6XBJ · Structure of human SMO-D384R 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 0.95
- 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 0.92
- 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 6XBJ · PDBe 6XBJ · UniProt Q99835 · UniProt P63096 · UniProt P62873 · UniProt P59768
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