MolNFT v1 · #123509 · protein
Crystal structure of acetylcholine binding protein (achbp) from aplysia californica in complex with alpha-conotoxin peia
5JME · Soluble acetylcholine receptor: “Crystal structure of acetylcholine binding protein (achbp) from aplysia californica in complex with…”. X-ray diffraction, 1 ligand (NH2), 20 pockets (best druggability 0.62). MolNFT v1 #123509 on…
- PDB
- 5JME
- Type
- protein
- Length
- 1,096 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor; Alpha-conotoxin peia from conus pergrandis
- UniProt
- Q8WSF8
- Ligands
- NH2
- Pockets
- 20 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 12% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 205 | 11% helix, 49% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 209 | 11% helix, 52% strand | Q8WSF8 |
| C, D | Soluble acetylcholine receptor | protein | 205 | 12% helix, 47% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 208 | 13% helix, 46% strand | Q8WSF8 |
| F, G, H, I | Alpha-conotoxin peia from conus pergrandis | protein | 16 | 44% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 4 copies · chains F, E, G, C, H, B, 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, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.62 | 0.75 | 46 | empty |
| 2 | 460 | 0.62 | 0.76 | 54 | empty |
| 3 | 101 | 0.57 | 0.85 | 22 | NH2 |
| 4 | 277 | 0.57 | 0.77 | 38 | empty |
| 5 | 294 | 0.56 | 0.76 | 38 | empty |
Interfaces
13 interfaces between chains.
- A–B · 1238 Ų buried · 14 hydrogen bonds · protein-protein
- D–E · 1155 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1153 Ų buried · 14 hydrogen bonds · protein-protein
- A–E · 1141 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1129 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide (disulfide).
Compared structures
- 5JME · Crystal structure of acetylcholine binding protein (AChBP) from Aplysia Californica in… · 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 5JME · PDBe 5JME · UniProt Q8WSF8
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