Research workbench
Cryo-EM structure of an orphan GPCR-Gi protein signaling complex
Analyse Cryo-EM structure of an orphan GPCR-Gi protein signaling complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8G05
- Type
- protein
- Length
- 1,140 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.0
- Source
- Homo sapiens
- Molecule
- G-protein coupled receptor 84; Guanine nucleotide-binding protein G(i) subunit alpha-1…
- UniProt
- Q9NQS5, P63096, P62873, P59768
- Ligands
- YI9, CLR
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · resolution 3.0 · 5 distinct chains · 30% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | G-protein coupled receptor 84 | protein | 286 | 62% helix, 3% strand | Q9NQS5 |
| A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | protein | 224 | 43% helix, 19% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 342 | 8% helix, 47% strand | P62873 |
| E | scFv16 | protein | 231 | 5% helix, 48% strand | — |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 56% helix, 0% strand | P59768 |
Ligands and binding sites
- YI9 · 6-(octylamino)pyrimidine-2,4(3H,5H)-dione · ligand · chains R
- CLR · Cholesterol · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 713 | 0.82 | 0.86 | 63 | empty |
| 2 | 120 | 0.80 | 0.98 | 27 | YI9 |
| 3 | 604 | 0.73 | 0.80 | 69 | empty |
| 4 | 229 | 0.59 | 0.80 | 39 | empty |
| 5 | 112 | 0.48 | 0.80 | 25 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2256 Ų buried · 19 hydrogen bonds · protein-protein
- R–A · 1182 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 1145 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 555 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 451 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 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 G against A, TM-score 0.97
- Q9NQS5 · AlphaFold monomer V2.0 prediction for G-protein coupled receptor 84 (Q9NQS5) · a predicted model of the same protein · chain R against A, TM-score 0.91
- 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 0.87
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 Q9NQS5
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 8G05 · PDBe 8G05 · UniProt Q9NQS5 · UniProt P63096 · UniProt P62873 · UniProt P59768
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