Research workbench
PF 06882961 bound to the glucagon-like peptide-1 receptor (GLP-1R):Gs complex
Analyse PF 06882961 bound to the glucagon-like peptide-1 receptor (GLP-1R):Gs complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7LCI
- Type
- protein
- Length
- 1,032 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.9
- Source
- Homo sapiens
- Molecule
- Glucagon-like peptide 1 receptor; Guanine nucleotide-binding protein G(s) subunit alpha…
- UniProt
- P43220, P63092, P62873, P59768
- Ligands
- UK4
- Pockets
- 13 · best druggability 0.85
Structure
electron microscopy · resolution 2.9 · 4 distinct chains · 41% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | Glucagon-like peptide 1 receptor | protein | 393 | 63% helix, 5% strand | P43220 |
| A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | protein | 244 | 47% helix, 16% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 7% helix, 46% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 57 | 54% helix, 0% strand | P59768 |
Ligands and binding sites
- UK4 · 2-[(4-{6-[(4-cyano-2-fluorophenyl)methoxy]pyridin-2-yl}piperidin-1-yl)methyl]-1-{[(2S)-oxetan-2-yl]methyl}-1H-benzimidazole-6-carboxylic acid · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 740 | 0.85 | 0.89 | 73 | UK4 |
| 2 | 680 | 0.82 | 0.86 | 58 | empty |
| 3 | 1141 | 0.72 | 0.76 | 77 | empty |
| 4 | 286 | 0.54 | 0.76 | 36 | empty |
| 5 | 172 | 0.53 | 0.79 | 30 | empty |
Interfaces
4 interfaces between chains.
- B–G · 2239 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1304 Ų buried · 10 hydrogen bonds · protein-protein
- R–A · 1011 Ų buried · 10 hydrogen bonds · protein-protein
- R–B · 253 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7LCI · Pf 06882961 bound to the glucagon-like peptide-1 receptor (glp-1R):GS complex · 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
- 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 G against A, TM-score 0.92
- 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 0.87
- P43220 · AlphaFold monomer V2.0 prediction for glucagon-like peptide 1 receptor (P43220) · a predicted model of the same protein · chain R against A, TM-score 0.81
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 P43220
- Every structure of UniProt P63092
- Every structure of UniProt P62873
- Every structure of UniProt P59768
- Elsewhere: RCSB PDB 7LCI · PDBe 7LCI · UniProt P43220 · UniProt P63092 · UniProt P62873 · UniProt P59768
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