Research workbench
Cryo-EM structure of the beclomethasone-bound adhesion receptor GPR97- go complex
Analyse Cryo-EM structure of the beclomethasone-bound adhesion receptor GPR97- go… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D76
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- 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, GXR
- Pockets
- 8 · best druggability 0.87
Structure
electron microscopy · 4 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(O) subunit alpha | protein | 215 | 42% helix, 13% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 41% strand | P62873 |
| G | 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 G3 | protein | 265 | 73% helix, 3% 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
- GXR · (8~{S},9~{R},10~{S},11~{S},13~{S},14~{S},16~{S}, 17~{R})-9-chloranyl-10,13,16-trimethyl-11,17-bis(oxidanyl)-17-(2-oxidanylethanoyl)-6,7,8,11,12,14, 15,16-octahydrocyclopenta[a]phenanthren-3-one · 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 | 899 | 0.87 | 0.88 | 75 | PLM, GXR |
| 2 | 823 | 0.83 | 0.85 | 65 | empty |
| 3 | 797 | 0.66 | 0.74 | 66 | empty |
| 4 | 115 | 0.46 | 0.79 | 23 | empty |
| 5 | 177 | 0.45 | 0.75 | 25 | empty |
Interfaces
4 interfaces between chains.
- B–G · 2126 Ų buried · 7 hydrogen bonds · protein-protein
- A–R · 1197 Ų buried · 3 hydrogen bonds · protein-protein
- A–B · 1123 Ų buried · 13 hydrogen bonds · protein-protein
- B–R · 178 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide, 1 lipid (disulfide, palmitoylation).
Compared structures
- 7D76 · Cryo-EM structure of the beclomethasone-bound adhesion receptor GPR97-Go complex · the same entry in another collection · chain A against A, 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 0.91
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 7D76 · PDBe 7D76 · UniProt P62873 · UniProt P59768
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