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Crystal structure of acetylcholine binding protein (achbp) from aplysia californica in complex with alpha-conotoxin buia
Analyse Crystal structure of acetylcholine binding protein (achbp) from aplysia… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EZ1
- Type
- protein
- Length
- 1,088 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor; Alpha-conotoxin buia
- UniProt
- Q8WSF8, P69657
- Ligands
- MN, NH2
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 203 | 9% helix, 51% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 203 | 11% helix, 48% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 207 | 13% helix, 46% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 208 | 13% helix, 48% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 202 | 9% helix, 52% strand | Q8WSF8 |
| K, L, M, N, O | Alpha-conotoxin buia | protein | 13 | 54% helix, 0% strand | P69657 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · chains C
- NH2 · Amino group · ion · 5 copies · chains B, K, A, L, E, M, D, N, C, O
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 390 | 0.62 | 0.77 | 52 | empty |
| 2 | 307 | 0.58 | 0.77 | 41 | empty |
| 3 | 298 | 0.55 | 0.76 | 39 | empty |
| 4 | 295 | 0.54 | 0.76 | 39 | empty |
| 5 | 257 | 0.54 | 0.77 | 37 | empty |
Interfaces
15 interfaces between chains.
- C–D · 1338 Ų buried · 16 hydrogen bonds · protein-protein
- D–E · 1318 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1305 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 1238 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1214 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 4EZ1 · Crystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in… · the same entry in another collection · chain O against O, TM-score 1.00
- P69657 · AlphaFold monomer V2.0 prediction for alpha-conotoxin buia (P69657) · a predicted model of the same protein · chain O against A, TM-score 0.46
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
- Every structure of UniProt P69657
- Elsewhere: RCSB PDB 4EZ1 · PDBe 4EZ1 · UniProt Q8WSF8 · UniProt P69657
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