Research workbench
Voltage-gated sodium channel Nav1.7 variant M4
Analyse Voltage-gated sodium channel Nav1.7 variant M4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8XMO
- Type
- protein
- Length
- 1,578 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.39
- Source
- Homo sapiens
- Molecule
- Sodium channel subunit beta-2; Sodium channel protein type 9 subunit alpha; Sodium…
- UniProt
- O60939, Q15858, Q07699
- Ligands
- LPE, PCW, NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.39 · 3 distinct chains · 59% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Sodium channel subunit beta-2 | protein | 119 | 3% helix, 46% strand | O60939 |
| A | Sodium channel protein type 9 subunit alpha | protein | 1286 | 69% helix, 3% strand | Q15858 |
| B | Sodium channel subunit beta-1 | protein | 173 | 22% helix, 32% strand | Q07699 |
Ligands and binding sites
- LPE · 1-O-octadecyl-sn-glycero-3-phosphocholine · ligand · 7 copies · chains A
- PCW · 1,2-dioleoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A, B
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 | 995 | 0.85 | 0.86 | 101 | empty |
| 2 | 605 | 0.72 | 0.79 | 41 | empty |
| 3 | 156 | 0.71 | 0.89 | 19 | empty |
| 4 | 629 | 0.71 | 0.79 | 75 | empty |
| 5 | 503 | 0.68 | 0.79 | 55 | empty |
Interfaces
2 interfaces between chains.
- A–B · 2101 Ų buried · 13 hydrogen bonds · protein-protein
- C–A · 234 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- Q15858 · AlphaFold monomer V2.0 prediction for sodium channel protein type 9 subunit alpha (Q15858) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O60939 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-2 (O60939) · a predicted model of the same protein · chain C against A, TM-score 0.97
- Q07699 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-1 (Q07699) · a predicted model of the same protein · chain B 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 O60939
- Every structure of UniProt Q15858
- Every structure of UniProt Q07699
- Elsewhere: RCSB PDB 8XMO · PDBe 8XMO · UniProt O60939 · UniProt Q15858 · UniProt Q07699
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