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The extra-helical binding site of GPR40 and the structural basis for allosteric agonism and incretin stimulation
Analyse The extra-helical binding site of GPR40 and the structural basis for allosteric… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5KW2
- Type
- protein
- Length
- 411 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Free fatty acid receptor 1,LYSOZYME,FREE fatty acid receptor 1
- EC
- 3.2.1.17
- UniProt
- O14842, D9IEF7
- Ligands
- 6XQ
- Pockets
- 4 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 75% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Free fatty acid receptor 1,LYSOZYME,FREE fatty acid receptor 1 (EC 3.2.1.17) | protein | 411 | 75% helix, 4% strand | O14842, D9IEF7 |
Ligands and binding sites
- 6XQ · (3~{S})-3-cyclopropyl-3-[2-[1-[2-[2,2-dimethylpropyl-(6-methylpyridin-2-yl)carbamoyl]-5-methoxy-phenyl]piperidin-4-yl]-1-benzofuran-6-yl]propanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 250 | 0.56 | 0.77 | 31 | empty |
| 2 | 171 | 0.48 | 0.76 | 27 | 6XQ |
| 3 | 72 | 0.39 | 0.79 | 13 | empty |
| 4 | 50 | 0.28 | 0.75 | 11 | empty |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5KW2 · The extra-helical binding site of GPR40 and the structural basis for allosteric agonism… · the same entry in another collection · chain A against A, TM-score 1.00
- O14842 · AlphaFold monomer V2.0 prediction for free fatty acid receptor 1 (O14842) · a predicted model of the same protein · chain A against A, TM-score 0.58
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 O14842
- Every structure of UniProt D9IEF7
- Elsewhere: RCSB PDB 5KW2 · PDBe 5KW2 · UniProt O14842 · UniProt D9IEF7
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