MolNFT v1 · #190319 · protein
Cryo-EM structure of the adhesion GPCR ADGRF1 in complex with minigi
7WU4 · Guanine nucleotide-binding protein G(I) subunit alpha-1: “Cryo-EM structure of the adhesion GPCR ADGRF1 in complex with minigi”. Electron microscopy, 2 ligands (CLR, K6G), 9 pockets (best druggability 0.82). MolNFT v1 #190319 on…
- PDB
- 7WU4
- Type
- protein
- Length
- 888 residues
- Chains
- 4
- 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
- A0A3B3IUA8, P63096, P62873, P59768, Q5T601
- Ligands
- CLR, K6G
- Pockets
- 9 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 207 | 47% helix, 14% strand | A0A3B3IUA8, P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 8% helix, 45% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 59% helix, 0% strand | P59768 |
| R | Adhesion G-protein coupled receptor F1 | protein | 286 | 67% helix, 2% strand | Q5T601 |
Ligands and binding sites
- CLR · Cholesterol · ligand · chains R
- K6G · [(2~{R})-2-oxidanyl-3-[oxidanyl-[2-(trimethyl-$l^{4}-azanyl)ethoxy]phosphoryl]oxy-propyl] hexadecanoate · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 706 | 0.82 | 0.85 | 60 | empty |
| 2 | 685 | 0.73 | 0.79 | 59 | empty |
| 3 | 280 | 0.64 | 0.81 | 30 | empty |
| 4 | 159 | 0.58 | 0.83 | 32 | empty |
| 5 | 104 | 0.51 | 0.81 | 16 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2155 Ų buried · 13 hydrogen bonds · protein-protein
- A–R · 1374 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 1182 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7WU4 · Cryo-EM structure of the adhesion GPCR ADGRF1 in complex with miniGi · 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 C against A, TM-score 0.93
- Q5T601 · AlphaFold monomer V2.0 prediction for adhesion G-protein coupled receptor F1 (Q5T601) · a predicted model of the same protein · chain R against A, TM-score 0.84
- 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 0.80
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 A0A3B3IUA8
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q5T601
- Elsewhere: RCSB PDB 7WU4 · PDBe 7WU4 · UniProt A0A3B3IUA8 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q5T601
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