MolNFT v1 · #154883 · protein
Cryo-EM structure of CB1-G protein complex
6KPG · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of CB1-G protein complex”. Electron microscopy, 1 ligand (8D0), 13 pockets (best druggability 0.86). MolNFT v1 #154883 on GenesisL1: 3D structure, binding…
- PDB
- 6KPG
- Type
- protein
- Length
- 1,135 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine nucleotide-binding…
- UniProt
- P63096, P62873, P59768, P21554
- Ligands
- 8D0
- Pockets
- 13 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 225 | 34% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 41% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 57% helix, 0% strand | P59768 |
| R | Cannabinoid receptor 1 | protein | 285 | 67% helix, 1% strand | P21554 |
| S | SCFV16 | protein | 231 | 3% helix, 43% strand | — |
Ligands and binding sites
- 8D0 · (6~{a}~{R},9~{R},10~{a}~{R})-9-(hydroxymethyl)-3-(8-isothiocyanato-2-methyl-octan-2-yl)-6,6-dimethyl-6~{a},7,8,9,10,10~{a}-hexahydrobenzo[c]chromen-1-ol · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 373 | 0.86 | 0.94 | 41 | 8D0 |
| 2 | 696 | 0.81 | 0.85 | 65 | empty |
| 3 | 794 | 0.72 | 0.78 | 66 | empty |
| 4 | 140 | 0.59 | 0.84 | 34 | empty |
| 5 | 186 | 0.55 | 0.80 | 32 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2272 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 1231 Ų buried · 15 hydrogen bonds · protein-protein
- A–R · 1167 Ų buried · 6 hydrogen bonds · protein-protein
- A–S · 637 Ų buried · 10 hydrogen bonds · protein-protein
- B–S · 494 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6KPG · Cryo-EM structure of CB1-G protein complex · the same entry in another collection · chain R against R, 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
- P21554 · AlphaFold monomer V2.0 prediction for cannabinoid receptor 1 (P21554) · 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 C 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 P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt P21554
- Elsewhere: RCSB PDB 6KPG · PDBe 6KPG · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P21554
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.