MolNFT v1 · #154882 · protein
Cryo-EM structure of a class a GPCR with G protein complex
6KPF · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of a class a GPCR with G protein complex”. Electron microscopy, 1 ligand (E3R), 10 pockets (best druggability 0.83). MolNFT v1 #154882 on GenesisL1: 3D…
- PDB
- 6KPF
- 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, P34972
- Ligands
- E3R
- Pockets
- 10 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 30% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 218 | 39% helix, 16% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 48% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 58% helix, 0% strand | P59768 |
| R | Cannabinoid receptor 2 | protein | 290 | 62% helix, 0% strand | P34972 |
| S | SCFV16 | protein | 232 | 4% helix, 47% strand | — |
Ligands and binding sites
- E3R · 7-[(6aR,9R,10aR)-1-Hydroxy-9-(hydroxymethyl)-6,6-dimethyl-6a,7,8,9,10,10a-hexahydro-6H-benzo[c]chromen-3-yl]- 7-methyloctanenitrile · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 289 | 0.83 | 0.93 | 39 | E3R |
| 2 | 729 | 0.83 | 0.86 | 68 | empty |
| 3 | 1170 | 0.71 | 0.75 | 75 | empty |
| 4 | 418 | 0.67 | 0.79 | 59 | empty |
| 5 | 65 | 0.54 | 0.87 | 23 | empty |
Interfaces
6 interfaces between chains.
- B–C · 2323 Ų buried · 23 hydrogen bonds · protein-protein
- A–R · 1209 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1167 Ų buried · 13 hydrogen bonds · protein-protein
- A–S · 627 Ų buried · 7 hydrogen bonds · protein-protein
- B–S · 481 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6KPF · Cryo-EM structure of a class A GPCR with G protein complex · 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 C against A, TM-score 0.95
- P34972 · AlphaFold monomer V2.0 prediction for cannabinoid receptor 2 (P34972) · a predicted model of the same protein · chain R against A, TM-score 0.94
- 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 0.83
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 P34972
- Elsewhere: RCSB PDB 6KPF · PDBe 6KPF · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt P34972
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