Research workbench
Structure of acid-sensing ion channel in complex with snake toxin
Analyse Structure of acid-sensing ion channel in complex with snake toxin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4NTW
- Type
- protein
- Length
- 588 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid-sensing ion channel 1; Neurotoxin mittx-alpha; Basic phospholipase A2 homolog tx-beta
- UniProt
- Q1XA76, G9I929, G9I930
- Ligands
- NAG, NA, CL
- Pockets
- 8 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid-sensing ion channel 1 | protein | 410 | 35% helix, 24% strand | Q1XA76 |
| B | Neurotoxin mittx-alpha | protein | 60 | 22% helix, 25% strand | G9I929 |
| C | Basic phospholipase A2 homolog tx-beta | protein | 118 | 48% helix, 4% strand | G9I930 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- NA · Sodium ion · metal · 3 copies · chains A, B, C
- CL · Chloride ion · ion · chains A
- P6G · Hexaethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 338 | 0.68 | 0.82 | 52 | NA |
| 2 | 162 | 0.55 | 0.80 | 35 | empty |
| 3 | 207 | 0.51 | 0.76 | 36 | empty |
| 4 | 96 | 0.41 | 0.77 | 19 | empty |
| 5 | 109 | 0.38 | 0.75 | 16 | P6G |
Interfaces
3 interfaces between chains.
- A–B · 697 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 576 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 502 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, cyclization).
Compared structures
- 4NTW · Structure of acid-sensing ion channel in complex with snake toxin · the same entry in another collection · chain A against A, TM-score 1.00
- G9I930 · AlphaFold monomer V2.0 prediction for basic phospholipase A2 homolog mittx-beta (G9I930) · a predicted model of the same protein · chain C against A, TM-score 0.99
- Q1XA76 · AlphaFold monomer V2.0 prediction for acid-sensing ion channel 1 (Q1XA76) · a predicted model of the same protein · chain A against A, TM-score 0.94
- G9I929 · AlphaFold monomer V2.0 prediction for kunitz-type neurotoxin mittx- alpha (G9I929) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 Q1XA76
- Every structure of UniProt G9I929
- Every structure of UniProt G9I930
- Elsewhere: RCSB PDB 4NTW · PDBe 4NTW · UniProt Q1XA76 · UniProt G9I929 · UniProt G9I930
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