Research workbench
Cryo-EM structure of human cannabinoid receptor 2-gi protein in complex with agonist win 55,212-2
Analyse Cryo-EM structure of human cannabinoid receptor 2-gi protein in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PT0
- Type
- protein
- Length
- 1,284 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cannabinoid receptor 2; Guanine nucleotide-binding protein G(I) subunit alpha-1; Guanine…
- UniProt
- P34972, P63096, P62873, P59768
- Ligands
- PLM, CLR, WI5
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Cannabinoid receptor 2 | protein | 298 | 82% helix, 1% strand | P34972 |
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 353 | 50% helix, 10% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 42% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 61 | 51% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 232 | 3% helix, 45% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 4 copies · chains R
- CLR · Cholesterol · ligand · 4 copies · chains R
- WI5 · {(3R)-5-methyl-3-[(morpholin-4-yl)methyl]-2,3-dihydro[1,4]oxazino[2,3,4-hi]indol-6-yl}(naphthalen-1-yl)methanone · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 468 | 0.87 | 0.93 | 47 | WI5 |
| 2 | 670 | 0.80 | 0.84 | 70 | empty |
| 3 | 392 | 0.78 | 0.88 | 61 | empty |
| 4 | 193 | 0.71 | 0.88 | 42 | empty |
| 5 | 222 | 0.64 | 0.83 | 31 | empty |
Interfaces
8 interfaces between chains.
- B–C · 2254 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1840 Ų buried · 16 hydrogen bonds · protein-protein
- R–A · 1560 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 693 Ų buried · 8 hydrogen bonds · protein-protein
- B–E · 500 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 6PT0 · Cryo-EM structure of human cannabinoid receptor 2-Gi protein in complex with agonist WIN… · the same entry in another collection · chain A against A, 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
- P34972 · AlphaFold monomer V2.0 prediction for cannabinoid receptor 2 (P34972) · a predicted model of the same protein · chain R against A, TM-score 0.92
- 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 0.89
- 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 0.55
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 P34972
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 6PT0 · PDBe 6PT0 · UniProt P34972 · UniProt P63096 · UniProt P62873 · UniProt P59768
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