MolNFT v1 · #78753 · protein
Ac-achbp ligand binding domain (not including beta 9-10 linker) mutated to human alpha-7 nachr
3SIO · Soluble acetylcholine receptor: “Ac-achbp ligand binding domain (not including beta 9-10 linker) mutated to human alpha-7 nachr”. X-ray diffraction, 4 ligands (MLK, NAG, MAN), 20 pockets (best druggability 0.75). MolNFT v1 #78753 on…
- PDB
- 3SIO
- Type
- protein
- Length
- 2,162 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- MLK, NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Soluble acetylcholine receptor | protein | 214 | 13% helix, 50% strand | Q8WSF8 |
| B, E, G, J | Soluble acetylcholine receptor | protein | 216 | 13% helix, 49% strand | Q8WSF8 |
| C, H | Soluble acetylcholine receptor | protein | 221 | 11% helix, 45% strand | Q8WSF8 |
| D, I | Soluble acetylcholine receptor | protein | 214 | 11% helix, 46% strand | Q8WSF8 |
Ligands and binding sites
- MLK · Methyllycaconitine · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains B, D, E, G, J, A, C, F, H, I
- MAN · alpha-D-mannopyranose · sugar · 14 copies
- BMA · beta-D-mannopyranose · sugar · 4 copies
- MRD · (4R)-2-methylpentane-2,4-diol · additive · 7 copies · chains A, B, C, D, E, F, G, H, I, J
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains C, D, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.75 | 0.78 | 64 | empty |
| 2 | 855 | 0.74 | 0.78 | 92 | MLK |
| 3 | 889 | 0.74 | 0.78 | 63 | empty |
| 4 | 1062 | 0.74 | 0.77 | 65 | empty |
| 5 | 733 | 0.73 | 0.79 | 88 | MRD, MLK |
Interfaces
24 interfaces between chains.
- D–E · 1421 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1390 Ų buried · 12 hydrogen bonds · protein-protein
- G–H · 1377 Ų buried · 13 hydrogen bonds · protein-protein
- F–G · 1357 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1345 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 14 glycan (disulfide, N-glycosylation).
Compared structures
- 3SIO · Ac-AChBP ligand binding domain (not including beta 9-10 linker) mutated to human alpha-7… · the same entry in another collection · chain A against A, TM-score 1.00
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 Q8WSF8
- Elsewhere: RCSB PDB 3SIO · PDBe 3SIO · UniProt Q8WSF8
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