MolNFT v1 · #101521 · protein
Cesium sites in the crystal structure of acid-sensing ion channel in complex with snake toxin
4NTY · Acid-sensing ion channel 1: “Cesium sites in the crystal structure of acid-sensing ion channel in complex with snake toxin”. X-ray diffraction, 2 ligands (CS, CL), 9 pockets (best druggability 0.63). MolNFT v1 #101521 on GenesisL1…
- PDB
- 4NTY
- Type
- protein
- Length
- 584 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
- CS, CL
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid-sensing ion channel 1 | protein | 406 | 34% helix, 25% strand | Q1XA76 |
| B | Neurotoxin mittx-alpha | protein | 60 | 17% helix, 25% strand | G9I929 |
| C | Basic phospholipase A2 homolog tx-beta | protein | 118 | 53% helix, 3% strand | G9I930 |
Ligands and binding sites
- CS · Cesium ion · metal · 15 copies · chains A, C, B
- CL · Chloride ion · ion · chains A
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 123 | 0.63 | 0.87 | 25 | CS |
| 2 | 191 | 0.57 | 0.80 | 28 | empty |
| 3 | 170 | 0.55 | 0.80 | 35 | empty |
| 4 | 222 | 0.52 | 0.76 | 38 | empty |
| 5 | 177 | 0.45 | 0.75 | 34 | empty |
Interfaces
3 interfaces between chains.
- A–B · 724 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 537 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 502 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 4NTY · Cesium sites in the crystal structure of acid-sensing ion channel in complex with snake… · the same entry in another collection · chain C against C, 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 0.95
- 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 4NTY · PDBe 4NTY · UniProt Q1XA76 · UniProt G9I929 · UniProt G9I930
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