Research workbench
Crystal structure of acachbp in complex with anatoxin
Analyse Crystal structure of acachbp in complex with anatoxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6SH0
- Type
- protein
- Length
- 2,059 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine binding protein
- UniProt
- Q8WSF8
- Ligands
- 4P0, NAG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D, E, F, G | Acetylcholine binding protein | protein | 205 | 11% helix, 50% strand | Q8WSF8 |
| B, H, J | Acetylcholine binding protein | protein | 206 | 10% helix, 50% strand | Q8WSF8 |
| I | Acetylcholine binding protein | protein | 211 | 9% helix, 52% strand | Q8WSF8 |
Ligands and binding sites
- 4P0 · 1-[(1R,6R)-9-azabicyclo[4.2.1]non-2-en-2-yl]ethanone · ligand · 10 copies · chains A, E, B, C, D, F, J, G, H, I
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, B, C, H, D, G, E, F, I, J
- ACT · Acetate ion · additive · 10 copies · chains A, B, C, D, F, G, J, H, I
- GOL · Glycerol · additive · 5 copies · chains A, B, C, D, E, I, J
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 | 96 | 0.71 | 0.94 | 23 | 4P0 |
| 2 | 77 | 0.71 | 0.95 | 21 | 4P0 |
| 3 | 308 | 0.68 | 0.83 | 48 | GOL, 4P0 |
| 4 | 317 | 0.68 | 0.82 | 49 | ACT, 4P0 |
| 5 | 272 | 0.68 | 0.83 | 49 | GOL, 4P0 |
Interfaces
17 interfaces between chains.
- I–J · 1456 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1426 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1423 Ų buried · 19 hydrogen bonds · protein-protein
- A–B · 1413 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1412 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 9 glycan (disulfide, N-glycosylation).
Compared structures
- 6SH0 · Crystal structure of AcAChBP in complex with anatoxin · 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 6SH0 · PDBe 6SH0 · UniProt Q8WSF8
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