Research workbench
Cryo-EM structure of ET-1 bound ETBR-DNGI complex
Analyse Cryo-EM structure of ET-1 bound ETBR-DNGI complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8XWQ
- Type
- protein
- Length
- 1,163 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.6
- Source
- Homo sapiens; Mus musculus
- Molecule
- Endothelin receptor type B; Endothelin-1; Guanine nucleotide-binding protein G(i) subunit…
- UniProt
- P24530, P05305, P63096, P62873, P59768
- Pockets
- 15 · best druggability 0.82
Structure
electron microscopy · resolution 4.6 · 6 distinct chains · 34% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Endothelin receptor type B | protein | 302 | 74% helix, 4% strand | P24530 |
| L | Endothelin-1 | protein | 21 | 33% helix, 5% strand | P05305 |
| A | Guanine nucleotide-binding protein G(i) subunit alpha-1 | protein | 218 | 44% helix, 13% strand | P63096 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 43% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 53 | 53% helix, 0% strand | P59768 |
| D | SCFV16 | protein | 231 | 5% helix, 45% strand | — |
Pockets
15 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.82 | 0.85 | 69 | empty |
| 2 | 1166 | 0.79 | 0.81 | 85 | empty |
| 3 | 59 | 0.72 | 0.98 | 18 | empty |
| 4 | 57 | 0.71 | 0.97 | 26 | empty |
| 5 | 173 | 0.62 | 0.84 | 32 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2103 Ų buried · 15 hydrogen bonds · protein-protein
- R–L · 1405 Ų buried · 16 hydrogen bonds · protein-protein
- R–A · 1135 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 1030 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 554 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 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
- P24530 · AlphaFold monomer V2.0 prediction for endothelin receptor type B (P24530) · 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 C against A, TM-score 0.93
- 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 0.82
- P05305 · AlphaFold monomer V2.0 prediction for endothelin-1 (P05305) · a predicted model of the same protein · chain L against A, TM-score 0.47
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 P24530
- Every structure of UniProt P05305
- Every structure of UniProt P63096
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 8XWQ · PDBe 8XWQ · UniProt P24530 · UniProt P05305 · UniProt P63096 · UniProt P62873 · UniProt P59768
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