Research workbench
Aplysia californica achbp in complex with 2-fluoro- (CARBAMOYLPYRIDINYL)DESCHLOROEPIBATIDINE analogue (1)
Analyse Aplysia californica achbp in complex with 2-fluoro… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QKK
- Type
- protein
- Length
- 2,059 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor
- UniProt
- Q8WSF8
- Ligands
- H92, OXL, NAG, PO4
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F, I | Soluble acetylcholine receptor | protein | 205 | 9% helix, 50% strand | Q8WSF8 |
| B, D, G, H, J | Soluble acetylcholine receptor | protein | 206 | 8% helix, 50% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 209 | 9% helix, 49% strand | Q8WSF8 |
Ligands and binding sites
- H92 · 4-[5-[(1~{R},2~{R},4~{S})-7-azabicyclo[2.2.1]heptan-2-yl]-2-fluoranyl-pyridin-3-yl]benzamide · ligand · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- OXL · Oxalate ion · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, D, I, J
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D, E, F, G, H, I, J
- EDO · 1,2-ethanediol · additive · 40 copies · chains A, E, B, C, D, F, J, 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 | 981 | 0.72 | 0.76 | 104 | EDO |
| 2 | 657 | 0.68 | 0.77 | 78 | EDO |
| 3 | 356 | 0.66 | 0.80 | 48 | H92, PO4, EDO |
| 4 | 334 | 0.66 | 0.80 | 39 | H92, PO4, EDO |
| 5 | 327 | 0.65 | 0.80 | 42 | H92, PO4, EDO |
Interfaces
15 interfaces between chains.
- A–E · 1410 Ų buried · 16 hydrogen bonds · protein-protein
- F–J · 1410 Ų buried · 18 hydrogen bonds · protein-protein
- G–H · 1405 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 1403 Ų buried · 17 hydrogen bonds · protein-protein
- D–E · 1401 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6QKK · Aplysia californica AChBP in complex with 2-Fluoro-(carbamoylpyridinyl)deschloroepibatidin… · the same entry in another collection · chain I against I, 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 6QKK · PDBe 6QKK · UniProt Q8WSF8
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