Research workbench
Cryoem structure of the glucagon receptor with a dual-agonist peptide
Analyse Cryoem structure of the glucagon receptor with a dual-agonist peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WHC
- Type
- protein
- Length
- 1,126 residues
- Chains
- 6
- 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, P47871
- Pockets
- 14 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 33% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 219 | 44% helix, 16% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 332 | 5% helix, 42% strand | P62873 |
| C | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 47 | 38% helix, 0% strand | P59768 |
| E | Dual-agonist peptide | protein | 29 | 93% helix, 0% strand | — |
| N | NANOBODY35 | protein | 128 | 5% helix, 43% strand | — |
| R | Glucagon receptor | protein | 371 | 57% helix, 3% strand | P47871 |
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 839 | 0.82 | 0.85 | 90 | empty |
| 2 | 1095 | 0.76 | 0.78 | 74 | empty |
| 3 | 585 | 0.75 | 0.82 | 77 | empty |
| 4 | 264 | 0.64 | 0.81 | 34 | empty |
| 5 | 174 | 0.61 | 0.83 | 30 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2057 Ų buried · 13 hydrogen bonds · protein-protein
- E–R · 1632 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 1522 Ų buried · 21 hydrogen bonds · protein-protein
- A–R · 1385 Ų buried · 14 hydrogen bonds · protein-protein
- A–N · 954 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 6WHC · CryoEM Structure of the glucagon receptor with a dual-agonist peptide · 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
- P47871 · AlphaFold monomer V2.0 prediction for glucagon receptor (P47871) · a predicted model of the same protein · chain R against A, TM-score 0.94
- 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 0.87
- P63092 · AlphaFold monomer V2.0 prediction for guanine nucleotide-binding protein G(S) subunit… · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P47871
- Elsewhere: RCSB PDB 6WHC · PDBe 6WHC · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt P47871
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