Research workbench
Cryo-EM structure of human NAV1.3/BETA1/BETA2-ICA121431
Analyse Cryo-EM structure of human NAV1.3/BETA1/BETA2-ICA121431 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W7F
- Type
- protein
- Length
- 1,424 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel subunit beta-1; Sodium channel subunit beta-2; Sodium channel protein type…
- UniProt
- Q07699, O60939, Q9NY46
- Ligands
- 6OU, 8DE, 9Z9, NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 57% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sodium channel subunit beta-1 | protein | 173 | 21% helix, 32% strand | Q07699 |
| C | Sodium channel subunit beta-2 | protein | 122 | 2% helix, 20% strand | O60939 |
| D | Sodium channel protein type 3 subunit alpha | protein | 1129 | 68% helix, 2% strand | Q9NY46 |
Ligands and binding sites
- 6OU · [(2~{R})-1-[2-azanylethoxy(oxidanyl)phosphoryl]oxy-3-hexadecanoyloxy-propan-2-yl] (~{Z})-octadec-9-enoate · ligand · 17 copies · chains D
- 8DE · 2,2-diphenyl-~{N}-[4-(1,3-thiazol-2-ylsulfamoyl) phenyl]ethanamide · ligand · chains D
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains D, B
- BMA · beta-D-mannopyranose · sugar · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1158 | 0.86 | 0.87 | 98 | empty |
| 2 | 509 | 0.73 | 0.82 | 75 | empty |
| 3 | 447 | 0.69 | 0.80 | 57 | empty |
| 4 | 73 | 0.68 | 0.93 | 16 | empty |
| 5 | 291 | 0.67 | 0.82 | 42 | empty |
Interfaces
2 interfaces between chains.
- B–D · 1993 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 320 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7W7F · Cryo-EM structure of human NaV1.3/beta1/beta2-ICA121431 · the same entry in another collection · chain B against B, TM-score 1.00
- Q9NY46 · AlphaFold monomer V2.0 prediction for sodium channel protein type 3 subunit alpha (Q9NY46) · a predicted model of the same protein · chain D 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
- 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 0.85
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 Q07699
- Every structure of UniProt O60939
- Every structure of UniProt Q9NY46
- Elsewhere: RCSB PDB 7W7F · PDBe 7W7F · UniProt Q07699 · UniProt O60939 · UniProt Q9NY46
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