Research workbench
Crystal structure of aplysia californica achbp in complex with alpha- conotoxin imi
Analyse Crystal structure of aplysia californica achbp in complex with alpha- conotoxin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2BYP
- Type
- protein
- Length
- 1,113 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Soluble acetylcholine receptor; Alpha-conotoxin imi
- UniProt
- Q8WSF8, P50983
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Soluble acetylcholine receptor | protein | 210 | 13% helix, 46% strand | Q8WSF8 |
| B | Soluble acetylcholine receptor | protein | 213 | 11% helix, 49% strand | Q8WSF8 |
| C | Soluble acetylcholine receptor | protein | 211 | 10% helix, 49% strand | Q8WSF8 |
| D | Soluble acetylcholine receptor | protein | 207 | 12% helix, 46% strand | Q8WSF8 |
| E | Soluble acetylcholine receptor | protein | 212 | 12% helix, 49% strand | Q8WSF8 |
| F, G, H, I, J | Alpha-conotoxin imi | protein | 12 | 50% helix, 0% strand | P50983 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 506 | 0.64 | 0.76 | 56 | empty |
| 2 | 389 | 0.60 | 0.76 | 49 | empty |
| 3 | 82 | 0.58 | 0.88 | 21 | empty |
| 4 | 337 | 0.57 | 0.76 | 40 | empty |
| 5 | 329 | 0.56 | 0.75 | 37 | empty |
Interfaces
15 interfaces between chains.
- B–C · 1332 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1316 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 1283 Ų buried · 13 hydrogen bonds · protein-protein
- D–E · 1261 Ų buried · 14 hydrogen bonds · protein-protein
- C–D · 1234 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide, 5 modified, 1 glycan (disulfide, nonstandard, N-glycosylation).
Compared structures
- 2BYP · Crystal structure of Aplysia californica AChBP in complex with alpha- conotoxin ImI · the same entry in another collection · chain J against J, TM-score 1.00
- P50983 · AlphaFold monomer V2.0 prediction for alpha-conotoxin imi (P50983) · a predicted model of the same protein · chain J against A, TM-score 0.68
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 P50983
- Elsewhere: RCSB PDB 2BYP · PDBe 2BYP · UniProt Q8WSF8 · UniProt P50983
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