Research workbench
Cryo-EM structure of the adhesion GPCR ADGRF1(H565A/T567A) in complex with minigi
Analyse Cryo-EM structure of the adhesion GPCR ADGRF1(H565A/T567A) 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
- 7WU5
- 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
- 8 · best druggability 0.82
Structure
electron microscopy · 4 distinct chains · 39% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(I) subunit alpha-1 | protein | 207 | 46% helix, 15% strand | A0A3B3IUA8, P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 6% helix, 48% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 54% helix, 0% strand | P59768 |
| R | Adhesion G-protein coupled receptor F1 | protein | 286 | 70% helix, 0% 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
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 770 | 0.82 | 0.86 | 63 | empty |
| 2 | 570 | 0.68 | 0.78 | 52 | empty |
| 3 | 344 | 0.66 | 0.80 | 36 | empty |
| 4 | 77 | 0.49 | 0.83 | 15 | empty |
| 5 | 178 | 0.45 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–C · 2163 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1203 Ų buried · 17 hydrogen bonds · protein-protein
- A–R · 1168 Ų buried · 12 hydrogen bonds · protein-protein
- B–R · 17 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7WU5 · Cryo-EM structure of the adhesion GPCR ADGRF1(H565A/T567A) 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 7WU5 · PDBe 7WU5 · UniProt A0A3B3IUA8 · UniProt P63096 · UniProt P62873 · UniProt P59768 · UniProt Q5T601
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