MolNFT v1 · #175962 · protein
Cryo-EM structure of the cortisol-bound adhesion receptor GPR97-go complex
7D77 · Guanine nucleotide-binding protein G(O) subunit alpha: “Cryo-EM structure of the cortisol-bound adhesion receptor GPR97-go complex”. Electron microscopy, 4 ligands (PLM, CLR, Y01), 10 pockets (best druggability 0.83). MolNFT v1…
- PDB
- 7D77
- Type
- protein
- Length
- 1,105 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(O) subunit alpha; Guanine nucleotide-binding protein…
- UniProt
- P62873, P59768
- Ligands
- PLM, CLR, Y01, HCY
- Pockets
- 10 · best druggability 0.83
Structure
electron microscopy · 5 distinct chains · 30% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(O) subunit alpha | protein | 215 | 38% helix, 17% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 50% helix, 0% strand | P59768 |
| R | Adhesion G protein-coupled receptor G3 | protein | 265 | 72% helix, 6% strand | — |
| S | SCFV16 | protein | 231 | 1% helix, 46% strand | — |
Ligands and binding sites
- PLM · Palmitic acid · ligand · 3 copies · chains A, R
- CLR · Cholesterol · ligand · 2 copies · chains R
- Y01 · Cholesterol hemisuccinate · ligand · chains R
- HCY · (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione · 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 838 | 0.83 | 0.85 | 62 | empty |
| 2 | 452 | 0.83 | 0.89 | 35 | HCY |
| 3 | 446 | 0.80 | 0.87 | 48 | PLM |
| 4 | 890 | 0.69 | 0.75 | 87 | empty |
| 5 | 412 | 0.67 | 0.80 | 64 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2117 Ų buried · 13 hydrogen bonds · protein-protein
- A–R · 1183 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1169 Ų buried · 15 hydrogen bonds · protein-protein
- A–S · 568 Ų buried · 6 hydrogen bonds · protein-protein
- B–S · 436 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide, 1 lipid (disulfide, palmitoylation).
Compared structures
- 7D77 · Cryo-EM structure of the cortisol-bound adhesion receptor GPR97-Go complex · the same entry in another collection · chain B against B, 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 1.00
- 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 0.94
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 P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7D77 · PDBe 7D77 · UniProt P62873 · UniProt P59768
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.