Research workbench
Cryo-EM structure of the R399-bound gpbar-gs complex
Analyse Cryo-EM structure of the R399-bound gpbar-gs complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XTQ
- Type
- protein
- Length
- 1,027 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(S) subunit alpha isoforms short; Guanine…
- UniProt
- P63092, P62873, P59768, Q8TDU6
- Ligands
- H8I
- Pockets
- 10 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 37% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 229 | 43% helix, 19% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 340 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 58 | 60% helix, 0% strand | P59768 |
| N | Nanobody-35 | protein | 127 | 5% helix, 43% strand | — |
| R | G-protein coupled bile acid receptor 1 | protein | 273 | 76% helix, 1% strand | Q8TDU6 |
Ligands and binding sites
- H8I · [2-(2,5-Dichloro-phenoxy)-pyridin-3-yl]-(3,4-dihydro-2H-quinolin-1-yl)-methanone · 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, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 290 | 0.86 | 0.96 | 23 | H8I |
| 2 | 891 | 0.84 | 0.86 | 76 | empty |
| 3 | 1019 | 0.79 | 0.81 | 92 | empty |
| 4 | 911 | 0.75 | 0.79 | 65 | empty |
| 5 | 332 | 0.65 | 0.81 | 48 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2276 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1475 Ų buried · 12 hydrogen bonds · protein-protein
- A–R · 1357 Ų buried · 14 hydrogen bonds · protein-protein
- A–N · 727 Ų buried · 3 hydrogen bonds · protein-protein
- B–N · 539 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7XTQ · Cryo-EM structure of the R399-bound GPBAR-Gs complex · 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
- Q8TDU6 · AlphaFold monomer V2.0 prediction for G-protein coupled bile acid receptor 1 (Q8TDU6) · a predicted model of the same protein · chain R against A, TM-score 0.95
- 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 P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Every structure of UniProt Q8TDU6
- Elsewhere: RCSB PDB 7XTQ · PDBe 7XTQ · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt Q8TDU6
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