Research workbench
Parallel homodimer structures of the extracellular domains of the voltage-gated sodium channel BETA4 subunit explain its role in cell- cell adhesion
Analyse Parallel homodimer structures of the extracellular domains of the voltage-gated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5XAX
- Type
- protein
- Length
- 238 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel subunit beta-4
- UniProt
- Q7M729
- Pockets
- 2 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel subunit beta-4 | protein | 118 | 3% helix, 55% strand | Q7M729 |
| B | Sodium channel subunit beta-4 | protein | 120 | 3% helix, 48% strand | Q7M729 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.40 | 0.78 | 26 | empty |
| 2 | 63 | 0.31 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1214 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5XAX · Parallel homodimer structures of the extracellular domains of the voltage-gated sodium… · the same entry in another collection · chain A against A, TM-score 1.00
- Q7M729 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-4 (Q7M729) · a predicted model of the same protein · chain A against A, TM-score 0.88
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 Q7M729
- Elsewhere: RCSB PDB 5XAX · PDBe 5XAX · UniProt Q7M729
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