Research workbench
Barium sites in the structure of a resting acid sensing ion channel
Analyse Barium sites in the structure of a resting acid sensing ion channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WKX
- 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, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 292 | 0.78 | 0.90 | 53 | empty |
| 2 | 391 | 0.78 | 0.87 | 42 | CL |
| 3 | 192 | 0.77 | 0.93 | 46 | empty |
| 4 | 604 | 0.75 | 0.82 | 64 | empty |
| 5 | 227 | 0.74 | 0.89 | 42 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2325 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2322 Ų buried · 23 hydrogen bonds · protein-protein
- C–B · 2182 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 5WKX · Barium sites in the structure of a resting acid sensing ion channel · 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 5WKX · PDBe 5WKX · UniProt Q1XA76
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