Research workbench
Structure of the glucagon receptor in complex with a glucagon analogue
Analyse Structure of the glucagon receptor in complex with a glucagon analogue in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YQZ
- Type
- protein
- Length
- 586 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor; Glucagon analogue
- EC
- 3.2.1.17
- UniProt
- P47871, D9IEF7
- Ligands
- NAG, PO4
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 69% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor (EC 3.2.1.17) | protein | 558 | 68% helix, 6% strand | P47871, D9IEF7 |
| P | Glucagon analogue | protein | 28 | 93% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains R
- PO4 · Phosphate ion · ion · chains R
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 6 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.76 | 0.85 | 51 | empty |
| 2 | 371 | 0.73 | 0.84 | 41 | empty |
| 3 | 158 | 0.70 | 0.89 | 32 | empty |
| 4 | 215 | 0.52 | 0.76 | 29 | empty |
| 5 | 185 | 0.47 | 0.75 | 24 | empty |
Interfaces
1 interface between chains.
- R–P · 1981 Ų buried · 20 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
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 P47871
- Every structure of UniProt D9IEF7
- Elsewhere: RCSB PDB 5YQZ · PDBe 5YQZ · UniProt P47871 · UniProt D9IEF7
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