Research workbench
Structure of a eukaryotic voltage-gated sodium channel at near atomic resolution
Analyse Structure of a eukaryotic voltage-gated sodium channel at near atomic resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5X0M
- Type
- protein
- Length
- 1,323 residues
- Chains
- 1
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein
- UniProt
- D0E0C2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 1 distinct chain · 62% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein | protein | 1323 | 62% helix, 3% strand | D0E0C2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1098 | 0.82 | 0.83 | 92 | empty |
| 2 | 685 | 0.69 | 0.76 | 78 | empty |
| 3 | 358 | 0.67 | 0.80 | 32 | empty |
| 4 | 571 | 0.67 | 0.76 | 51 | empty |
| 5 | 101 | 0.64 | 0.89 | 21 | empty |
Modifications
Observed in the structure: 7 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 5X0M · Structure of a eukaryotic voltage-gated sodium channel at near atomic resolution · the same entry in another collection · chain A against A, TM-score 1.00
- D0E0C2 · AlphaFold monomer V2.0 prediction for sodium channel protein PAFPC1 (D0E0C2) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 D0E0C2
- Elsewhere: RCSB PDB 5X0M · PDBe 5X0M · UniProt D0E0C2
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