MolNFT v1 · #139415 · protein
Structure of the full-length glucagon class B G protein-coupled receptor
5XF1 · Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor: “Structure of the full-length glucagon class B G protein-coupled receptor”. X-ray diffraction, 2 ligands (97V, NAG), 19 pockets (best druggability 0.81). MolNFT v1 #139415 on GenesisL1…
- PDB
- 5XF1
- Type
- protein
- Length
- 1,930 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor; Antibody MAB1 heavy chain; Antibody MAB1…
- EC
- 3.2.1.17
- UniProt
- P47871, D9IEF7
- Ligands
- 97V, NAG
- Pockets
- 19 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 46% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor (EC 3.2.1.17) | protein | 544 | 61% helix, 7% strand | P47871, D9IEF7 |
| B | Glucagon RECEPTOR,ENDOLYSIN,GLUCAGON receptor (EC 3.2.1.17) | protein | 496 | 65% helix, 7% strand | P47871, D9IEF7 |
| C, H | Antibody MAB1 heavy chain | protein | 231 | 4% helix, 54% strand | — |
| D, L | Antibody MAB1 light chain | protein | 214 | 7% helix, 50% strand | — |
Ligands and binding sites
- 97V · 4-{[(4-cyclohexylphenyl){[3-(methylsulfonyl) phenyl]carbamoyl}amino]methyl}-N-(1H-tetrazol-5-yl) benzamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.81 | 0.82 | 89 | empty |
| 2 | 923 | 0.74 | 0.77 | 67 | empty |
| 3 | 461 | 0.70 | 0.81 | 47 | empty |
| 4 | 278 | 0.64 | 0.81 | 36 | empty |
| 5 | 391 | 0.62 | 0.77 | 45 | empty |
Interfaces
10 interfaces between chains.
- C–D · 1988 Ų buried · 19 hydrogen bonds · protein-protein
- H–L · 1956 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 974 Ų buried · 13 hydrogen bonds · protein-protein
- B–H · 953 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 829 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 5XF1 · Structure of the Full-length glucagon class B G protein-coupled receptor · the same entry in another collection · chain L against L, TM-score 1.00
- P47871 · AlphaFold monomer V2.0 prediction for glucagon receptor (P47871) · a predicted model of the same protein · chain B against A, TM-score 0.51
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 5XF1 · PDBe 5XF1 · UniProt P47871 · UniProt D9IEF7
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