MolNFT v1 · #187704 · protein
Molecular mechanism of the the wake-promoting agent tak-925
7SR8 · A modified guanine nucleotide-binding protein G(Q) subunit…: “Molecular mechanism of the the wake-promoting agent tak-925”. Electron microscopy, 2 ligands (OLA, A6F), 16 pockets (best druggability 0.81). MolNFT v1 #187704 on…
- PDB
- 7SR8
- Type
- protein
- Length
- 1,141 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- A modified guanine nucleotide-binding protein G(Q) subunit alpha; Guanine…
- UniProt
- P62873, P59768, Q548Y0
- Ligands
- OLA, A6F
- Pockets
- 16 · best druggability 0.81
Structure
electron microscopy · 5 distinct chains · 34% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | A modified guanine nucleotide-binding protein G(Q) subunit alpha | protein | 226 | 42% helix, 17% strand | — |
| B | Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta-1 | protein | 339 | 9% helix, 47% strand | P62873 |
| G | Guanine nucleotide-binding protein G(I)/G(S)/G(O) subunit gamma-2 | protein | 59 | 56% helix, 0% strand | P59768 |
| E | SCFV16 | protein | 234 | 5% helix, 50% strand | — |
| R | Hypocretin receptor type 2 | protein | 283 | 78% helix, 4% strand | Q548Y0 |
Ligands and binding sites
- OLA · Oleic acid · ligand · 4 copies · chains R
- A6F · methyl (2R,3S)-3-[(methanesulfonyl)amino]-2-({[(1s,4S)-4-phenylcyclohexyl]oxy}methyl)piperidine-1-carboxylate · ligand · chains R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 726 | 0.81 | 0.85 | 55 | A6F |
| 2 | 682 | 0.81 | 0.85 | 62 | empty |
| 3 | 826 | 0.74 | 0.78 | 76 | empty |
| 4 | 59 | 0.59 | 0.91 | 14 | empty |
| 5 | 204 | 0.58 | 0.80 | 30 | empty |
Interfaces
6 interfaces between chains.
- B–G · 2130 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1387 Ų buried · 9 hydrogen bonds · protein-protein
- A–R · 1088 Ų buried · 10 hydrogen bonds · protein-protein
- A–E · 552 Ų buried · 9 hydrogen bonds · protein-protein
- B–E · 478 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 7SR8 · Molecular mechanism of the the wake-promoting agent TAK-925 · the same entry in another collection · chain B against B, 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 0.83
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 Q548Y0
- Elsewhere: RCSB PDB 7SR8 · PDBe 7SR8 · UniProt P62873 · UniProt P59768 · UniProt Q548Y0
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