Research workbench
Crystal structure of mutant achbp in complex with tropisetron (T53F, Q74R, Y110A, I135S, G162E)
Analyse Crystal structure of mutant achbp in complex with tropisetron (T53F, Q74R… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OAJ
- Type
- protein
- Length
- 2,080 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- TKT, NAG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, E, F, H, I | Soluble acetylcholine receptor | protein | 206 | 9% helix, 51% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 221 | 9% helix, 51% strand | Q8WSF8 |
| C, G | Soluble acetylcholine receptor | protein | 205 | 9% helix, 53% strand | Q8WSF8 |
| J | Soluble acetylcholine receptor | protein | 213 | 9% helix, 50% strand | Q8WSF8 |
Ligands and binding sites
- TKT · (3-endo)-8-methyl-8-azabicyclo[3.2.1]oct-3-yl 1H-indole-3-carboxylate · ligand · 2 copies · chains D, E, F, J
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, E, J, H, I
- EDO · 1,2-ethanediol · additive · 42 copies · chains A, B, E, C, D, F, G, J, H, I
- FLC · Citrate anion · additive · 3 copies · chains C, D, G, 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 | 649 | 0.71 | 0.78 | 62 | EDO |
| 2 | 584 | 0.69 | 0.78 | 61 | EDO |
| 3 | 547 | 0.68 | 0.78 | 52 | FLC, EDO |
| 4 | 293 | 0.68 | 0.83 | 52 | TKT |
| 5 | 500 | 0.67 | 0.78 | 43 | EDO |
Interfaces
19 interfaces between chains.
- A–B · 1951 Ų buried · 25 hydrogen bonds · protein-protein
- I–J · 1623 Ų buried · 19 hydrogen bonds · protein-protein
- F–J · 1366 Ų buried · 17 hydrogen bonds · protein-protein
- H–I · 1285 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1278 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
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 5OAJ · PDBe 5OAJ · UniProt Q8WSF8
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