Research workbench
Structure of the human voltage-gated sodium channel NAV1.4 in complex with BETA1
Analyse Structure of the human voltage-gated sodium channel NAV1.4 in complex with BETA1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6AGF
- Type
- protein
- Length
- 1,311 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel protein type 4 subunit alpha; Sodium channel subunit beta-1
- UniProt
- P35499, Q07699
- Ligands
- 6OU, 9Z9, NAG, BMA
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 2 distinct chains · 60% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sodium channel protein type 4 subunit alpha | protein | 1138 | 65% helix, 2% strand | P35499 |
| B | Sodium channel subunit beta-1 | protein | 173 | 23% helix, 29% strand | Q07699 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 6 copies · chains A
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 618 | 0.81 | 0.86 | 59 | 6OU, 9Z9 |
| 2 | 545 | 0.70 | 0.79 | 63 | empty |
| 3 | 160 | 0.67 | 0.87 | 24 | empty |
| 4 | 294 | 0.65 | 0.81 | 20 | empty |
| 5 | 114 | 0.63 | 0.87 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 2021 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6AGF · Structure of the human voltage-gated sodium channel Nav1.4 in complex with beta1 · the same entry in another collection · chain A against A, TM-score 1.00
- P35499 · AlphaFold monomer V2.0 prediction for sodium channel protein type 4 subunit alpha (P35499) · a predicted model of the same protein · chain A against A, TM-score 0.98
- 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 0.90
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 P35499
- Every structure of UniProt Q07699
- Elsewhere: RCSB PDB 6AGF · PDBe 6AGF · UniProt P35499 · UniProt Q07699
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