MolNFT v1 · #178260 · protein
Ghrelin-bound ghrelin receptor in complex with gq
7F9Y · Engineered G-alpha-Q subunit: “Ghrelin-bound ghrelin receptor in complex with gq”. Electron microscopy, 2 ligands (CLR, OCA), 12 pockets (best druggability 0.84). MolNFT v1 #178260 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7F9Y
- Type
- protein
- Length
- 1,051 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Engineered G-alpha-Q subunit; Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit…
- UniProt
- P62873, Q9UBU3, P59768
- Ligands
- CLR, OCA
- Pockets
- 12 · best druggability 0.84
Structure
electron microscopy · 6 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Engineered G-alpha-Q subunit | protein | 228 | 49% helix, 18% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 9% helix, 48% strand | P62873 |
| C | Ghrelin-28 | protein | 15 | 27% helix, 0% strand | Q9UBU3 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 60% helix, 0% strand | P59768 |
| N | NB35 | protein | 128 | 7% helix, 46% strand | — |
| R | Soluble cytochrome B562 | protein | 285 | 76% helix, 3% strand | — |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains R
- OCA · Octanoic acid (caprylic acid) · ligand · chains C, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 955 | 0.84 | 0.85 | 84 | empty |
| 2 | 1149 | 0.76 | 0.79 | 76 | empty |
| 3 | 1059 | 0.76 | 0.78 | 74 | empty |
| 4 | 624 | 0.74 | 0.81 | 68 | empty |
| 5 | 80 | 0.73 | 0.96 | 21 | OCA |
Interfaces
7 interfaces between chains.
- B–G · 2242 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1448 Ų buried · 20 hydrogen bonds · protein-protein
- A–R · 1044 Ų buried · 9 hydrogen bonds · protein-protein
- A–N · 815 Ų buried · 9 hydrogen bonds · protein-protein
- C–R · 812 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent, 1 disulfide (covalent ligand, disulfide).
Compared structures
- 7F9Y · ghrelin-bound ghrelin receptor in complex with Gq · 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
- 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 0.93
- Q9UBU3 · AlphaFold monomer V2.0 prediction for appetite-regulating hormone (Q9UBU3) · a predicted model of the same protein · chain C against A, TM-score 0.29
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 Q9UBU3
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7F9Y · PDBe 7F9Y · UniProt P62873 · UniProt Q9UBU3 · UniProt P59768
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