Research workbench
Molecular mechanism and structural basis of small-molecule modulation of acid-sensing ion channel 1 (ASIC1)
Analyse Molecular mechanism and structural basis of small-molecule modulation of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X9H
- Type
- protein
- Length
- 1,222 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acid-sensing ion channel 1
- UniProt
- Q1XA76
- Ligands
- UZG, NAG, NA
- Pockets
- 13 · best druggability 0.89
Structure
x-ray diffraction · 3 distinct chains · 35% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Acid-sensing ion channel 1 | protein | 409 | 34% helix, 26% strand | Q1XA76 |
| B | Acid-sensing ion channel 1 | protein | 410 | 36% helix, 26% strand | Q1XA76 |
| C | Acid-sensing ion channel 1 | protein | 403 | 34% helix, 26% strand | Q1XA76 |
Ligands and binding sites
- UZG · 2-[4-(3,4-dimethoxyphenoxy)phenyl]-1H-benzimidazole-6-carboximidamide · ligand · 3 copies · chains A, B, C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B, C
- NA · Sodium ion · metal · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.89 | 0.91 | 194 | empty |
| 2 | 1047 | 0.86 | 0.87 | 83 | UZG |
| 3 | 609 | 0.84 | 0.89 | 69 | UZG |
| 4 | 426 | 0.82 | 0.90 | 60 | UZG |
| 5 | 366 | 0.77 | 0.87 | 43 | NA |
Interfaces
3 interfaces between chains.
- A–B · 2596 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 2485 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 2460 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 21 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 6X9H · Molecular mechanism and structural basis of small-molecule modulation of acid-sensing ion… · 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 B against A, TM-score 0.98
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 6X9H · PDBe 6X9H · UniProt Q1XA76
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