MolNFT v1 · #179854 · protein
Semaglutide-bound glucagon-like peptide-1 (glp-1) receptor in complex with gs protein
7KI0 · Guanine nucleotide-binding protein G(S) subunit alpha…: “Semaglutide-bound glucagon-like peptide-1 (glp-1) receptor in complex with gs protein”. Electron microscopy, 1 ligand (WF1), 13 pockets (best druggability 0.82). MolNFT v1…
- PDB
- 7KI0
- Type
- protein
- Length
- 1,143 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, P43220
- Ligands
- WF1
- Pockets
- 13 · best druggability 0.82
Structure
electron microscopy · 6 distinct chains · 38% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(S) subunit alpha isoforms short | protein | 209 | 44% helix, 19% strand | P63092 |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 56 | 59% helix, 0% strand | P59768 |
| N | NB35 | protein | 126 | 7% helix, 44% strand | — |
| P | Semaglutide | protein | 30 | 87% helix, 0% strand | — |
| R | Glucagon-like peptide 1 receptor | protein | 384 | 66% helix, 4% strand | P43220 |
Ligands and binding sites
- WF1 · 17-amino-10-oxo-3,6,12,15-tetraoxa-9-azaheptadecan-1-oic acid · ligand · chains P, 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.82 | 0.86 | 57 | empty |
| 2 | 866 | 0.76 | 0.80 | 56 | empty |
| 3 | 1068 | 0.76 | 0.78 | 85 | empty |
| 4 | 58 | 0.67 | 0.95 | 18 | empty |
| 5 | 138 | 0.67 | 0.88 | 24 | empty |
Interfaces
7 interfaces between chains.
- B–G · 2228 Ų buried · 19 hydrogen bonds · protein-protein
- P–R · 1693 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1502 Ų buried · 33 hydrogen bonds · protein-protein
- A–R · 1056 Ų buried · 8 hydrogen bonds · protein-protein
- A–N · 829 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent, 1 modified (disulfide, covalent ligand, nonstandard).
Compared structures
- 7KI0 · Semaglutide-bound Glucagon-Like Peptide-1 (GLP-1) Receptor in Complex with Gs protein · 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 1.00
- 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 0.96
- 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 0.78
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 P43220
- Elsewhere: RCSB PDB 7KI0 · PDBe 7KI0 · UniProt P63092 · UniProt P62873 · UniProt P59768 · UniProt P43220
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