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Structural mechanisms for alpha-conotoxin selectivity at the human ALPHA3BETA4 nicotinic acetylcholine receptor
Analyse Structural mechanisms for alpha-conotoxin selectivity at the human ALPHA3BETA4… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T90
- Type
- protein
- Length
- 1,090 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acetylcholine-binding protein; Lsia
- UniProt
- P58154
- Ligands
- NH2
- Pockets
- 16 · best druggability 0.70
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acetylcholine-binding protein | protein | 205 | 8% helix, 46% strand | P58154 |
| B | Acetylcholine-binding protein | protein | 197 | 8% helix, 48% strand | P58154 |
| C | Acetylcholine-binding protein | protein | 203 | 8% helix, 47% strand | P58154 |
| D | Acetylcholine-binding protein | protein | 200 | 8% helix, 47% strand | P58154 |
| E | Acetylcholine-binding protein | protein | 204 | 8% helix, 47% strand | P58154 |
| F, G, H | Lsia | protein | 17 | 59% helix, 0% strand | — |
| I, J | Lsia | protein | 15 | 67% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 5 copies · chains F, B, G, E, H, D, I, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 431 | 0.70 | 0.81 | 51 | empty |
| 2 | 394 | 0.69 | 0.81 | 47 | empty |
| 3 | 438 | 0.69 | 0.80 | 50 | empty |
| 4 | 457 | 0.69 | 0.79 | 52 | empty |
| 5 | 405 | 0.68 | 0.80 | 48 | empty |
Interfaces
15 interfaces between chains.
- A–C · 1263 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1238 Ų buried · 15 hydrogen bonds · protein-protein
- A–E · 1220 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 1215 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1146 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 disulfide (disulfide).
Compared structures
- 5T90 · Structural mechanisms for alpha-conotoxin selectivity at the human alpha3beta4 nicotinic… · the same entry in another collection · chain J against J, TM-score 1.00
- P58154 · AlphaFold monomer V2.0 prediction for acetylcholine-binding protein (P58154) · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P58154
- Elsewhere: RCSB PDB 5T90 · PDBe 5T90 · UniProt P58154
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