MolNFT v1 · #138489 · protein
Structure of an acid sensing ion channel in a resting state with barium
5WKU · Acid-sensing ion channel 1: “Structure of an acid sensing ion channel in a resting state with barium”. X-ray diffraction, 3 ligands (NAG, BA, CL), 15 pockets (best druggability 0.81). MolNFT v1 #138489 on GenesisL1: 3D structure…
- PDB
- 5WKU
- 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
- 15 · best druggability 0.81
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
15 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 463 | 0.81 | 0.88 | 64 | empty |
| 2 | 352 | 0.80 | 0.89 | 61 | empty |
| 3 | 205 | 0.78 | 0.93 | 49 | empty |
| 4 | 397 | 0.77 | 0.86 | 45 | CL |
| 5 | 598 | 0.76 | 0.82 | 63 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2328 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2326 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
- 5WKU · Structure of an acid sensing ion channel in a resting state with barium · the same entry in another collection · chain A against A, 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 5WKU · PDBe 5WKU · UniProt Q1XA76
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