Research workbench
Crystal structure of achbp from aplysia californica in complex with lobeline
Analyse Crystal structure of achbp from aplysia californica in complex with lobeline in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BYS
- Type
- protein
- Length
- 2,046 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein
- UniProt
- Q8WSF8
- Ligands
- LOB
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 10% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 205 | 9% helix, 52% strand | Q8WSF8 |
| B, I | Acetylcholine-binding protein | protein | 206 | 11% helix, 50% strand | Q8WSF8 |
| C | Acetylcholine-binding protein | protein | 203 | 9% helix, 54% strand | Q8WSF8 |
| D | Acetylcholine-binding protein | protein | 205 | 10% helix, 50% strand | Q8WSF8 |
| E | Acetylcholine-binding protein | protein | 206 | 11% helix, 53% strand | Q8WSF8 |
| F, J | Acetylcholine-binding protein | protein | 204 | 9% helix, 51% strand | Q8WSF8 |
| G | Acetylcholine-binding protein | protein | 203 | 9% helix, 54% strand | Q8WSF8 |
| H | Acetylcholine-binding protein | protein | 204 | 10% helix, 53% strand | Q8WSF8 |
Ligands and binding sites
- LOB · Lobeline · ligand · 10 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 | 1020 | 0.78 | 0.80 | 113 | LOB |
| 2 | 370 | 0.76 | 0.86 | 59 | LOB |
| 3 | 507 | 0.75 | 0.83 | 83 | LOB |
| 4 | 424 | 0.74 | 0.84 | 67 | LOB |
| 5 | 423 | 0.74 | 0.84 | 64 | LOB |
Interfaces
11 interfaces between chains.
- A–E · 1479 Ų buried · 17 hydrogen bonds · protein-protein
- F–J · 1380 Ų buried · 17 hydrogen bonds · protein-protein
- B–C · 1375 Ų buried · 19 hydrogen bonds · protein-protein
- F–G · 1370 Ų buried · 19 hydrogen bonds · protein-protein
- I–J · 1364 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 2BYS · CRYSTAL STRUCTURE OF ACHBP FROM APLYSIA CALIFORNICA IN complex with lobeline · 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 2BYS · PDBe 2BYS · UniProt Q8WSF8
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