Research workbench
Coupling specificity of heterotrimeric go to the serotonin 5-HT1B receptor
Analyse Coupling specificity of heterotrimeric go to the serotonin 5-HT1B receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G79
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1; Guanine…
- UniProt
- P62873, P59768, P09471, A0A0P7W0C8, P28222
- Ligands
- EP5
- Pockets
- 8 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 44% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 333 | 8% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 54% helix, 0% strand | P59768 |
| A | Guanine nucleotide-binding protein G(O) subunit alpha | protein | 209 | 50% helix, 15% strand | P09471, A0A0P7W0C8 |
| S | 5-hydroxytryptamine receptor 1B | protein | 262 | 84% helix, 0% strand | P28222 |
Ligands and binding sites
- EP5 · 2-[5-[2-[4-(4-cyanophenyl)piperazin-1-yl]-2-oxidanylidene-ethoxy]-1~{H}-indol-3-yl]ethylazanium · ligand · chains S
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 | 649 | 0.79 | 0.84 | 61 | empty |
| 2 | 379 | 0.75 | 0.85 | 42 | EP5 |
| 3 | 752 | 0.69 | 0.76 | 86 | empty |
| 4 | 67 | 0.47 | 0.83 | 19 | empty |
| 5 | 142 | 0.42 | 0.75 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–G · 1601 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 1093 Ų buried · 11 hydrogen bonds · protein-protein
- A–S · 841 Ų buried · 3 hydrogen bonds · protein-protein
- B–S · 21 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6G79 · Coupling specificity of heterotrimeric Go to the serotonin 5-HT1B receptor · the same entry in another collection · chain S against S, 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 0.95
- P28222 · AlphaFold monomer V2.0 prediction for 5-hydroxytryptamine receptor 1B (P28222) · a predicted model of the same protein · chain S against A, TM-score 0.94
- P09471 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(O) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.77
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
- Every structure of UniProt P09471
- Every structure of UniProt A0A0P7W0C8
- Every structure of UniProt P28222
- Elsewhere: RCSB PDB 6G79 · PDBe 6G79 · UniProt P62873 · UniProt P59768 · UniProt P09471 · UniProt A0A0P7W0C8 · UniProt P28222
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