MolNFT v1 · #138493 · protein
Bromide sites in the structure of an acid sensing ion channel in a resting state
5WKY · Acid-sensing ion channel 1: “Bromide sites in the structure of an acid sensing ion channel in a resting state”. X-ray diffraction, 3 ligands (NAG, BA, CL), 18 pockets (best druggability 0.78). MolNFT v1 #138493 on GenesisL1: 3D…
- PDB
- 5WKY
- Type
- protein
- Length
- 1,249 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid-sensing ion channel 1
- UniProt
- Q1XA76
- Ligands
- NAG, BA, CL
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid-sensing ion channel 1 | protein | 417 | 35% helix, 25% strand | Q1XA76 |
| C | Acid-sensing ion channel 1 | protein | 414 | 35% helix, 25% strand | Q1XA76 |
| B | Acid-sensing ion channel 1 | protein | 418 | 35% helix, 25% strand | Q1XA76 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains B, A, C
- BA · Barium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.78 | 0.87 | 41 | empty |
| 2 | 271 | 0.77 | 0.90 | 43 | empty |
| 3 | 591 | 0.76 | 0.82 | 65 | empty |
| 4 | 399 | 0.75 | 0.85 | 55 | empty |
| 5 | 239 | 0.75 | 0.89 | 51 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2329 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2327 Ų buried · 23 hydrogen bonds · protein-protein
- C–B · 2180 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5WKY · Bromide sites in the structure of an acid sensing ion channel in a resting state · the same entry in another collection · chain B against B, TM-score 1.00
- 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 0.97
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
- Elsewhere: RCSB PDB 5WKY · PDBe 5WKY · UniProt Q1XA76
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