Research workbench
GPR119-Gs-APD668 complex
Analyse GPR119-Gs-APD668 complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XZ6
- Type
- protein
- Length
- 1,052 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Escherichia coli; Homo sapiens; Lama glama
- Molecule
- Guanine nucleotide-binding protein G(s) subunit alpha isoforms short; Guanine…
- UniProt
- P62873, P59768, P0ABE7, Q8TDV5
- Ligands
- I7J
- Pockets
- 14 · best druggability 0.81
Structure
electron microscopy · resolution 2.8 · 5 distinct chains · 41% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Guanine nucleotide-binding protein G(s) subunit alpha isoforms short | protein | 237 | 50% helix, 17% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 338 | 8% 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 |
| N | Nanobody35 | protein | 128 | 5% helix, 45% strand | — |
| R | Soluble cytochrome b562,Glucose-dependent insulinotropic receptor | protein | 292 | 85% helix, 1% strand | P0ABE7, Q8TDV5 |
Ligands and binding sites
- I7J · Propan-2-yl 4-[1-(2-fluoranyl-4-methylsulfonyl-phenyl) pyrazolo[3,4-d]pyrimidin-4-yl]oxypiperidine-1-carboxylate · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 505 | 0.81 | 0.87 | 56 | empty |
| 2 | 217 | 0.78 | 0.92 | 39 | I7J |
| 3 | 1199 | 0.78 | 0.80 | 72 | empty |
| 4 | 673 | 0.76 | 0.81 | 58 | empty |
| 5 | 78 | 0.69 | 0.95 | 21 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2268 Ų buried · 20 hydrogen bonds · protein-protein
- A–R · 1663 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1547 Ų buried · 32 hydrogen bonds · protein-protein
- A–N · 1034 Ų buried · 15 hydrogen bonds · protein-protein
- B–N · 653 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7XZ6 · GPR119-gs-APD668 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 0.93
- Q8TDV5 · AlphaFold monomer V2.0 prediction for glucose-dependent insulinotropic receptor (Q8TDV5) · a predicted model of the same protein · chain R against A, TM-score 0.92
- P0ABE7 · AlphaFold monomer V2.0 prediction for soluble cytochrome B562 (P0ABE7) · a predicted model of the same protein · chain R against A, TM-score 0.26
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 P62873
- Every structure of UniProt P59768
- Every structure of UniProt P0ABE7
- Every structure of UniProt Q8TDV5
- Elsewhere: RCSB PDB 7XZ6 · PDBe 7XZ6 · UniProt P62873 · UniProt P59768 · UniProt P0ABE7 · UniProt Q8TDV5
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