Research workbench
Cryo-EM structure of human NAV1.3/BETA1/BETA2-bulleyaconitinea
Analyse Cryo-EM structure of human NAV1.3/BETA1/BETA2-bulleyaconitinea in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7W77
- 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, 9Z9, 966, NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Sodium channel subunit beta-1 | protein | 173 | 23% helix, 32% strand | Q07699 |
| C | Sodium channel subunit beta-2 | protein | 122 | 5% helix, 41% strand | O60939 |
| D | Sodium channel protein type 3 subunit alpha | protein | 1129 | 69% 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 · 16 copies · chains D
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · 3 copies · chains D
- 966 · [(1S,2R,3R,4R,5R,6S,8R,9S,13S,16S,17R,18R)-11-ethyl-5-hydroxy-6,16,18-trimethoxy-4-(4-methoxybenzoyl)-13-(methoxymethyl)-11-azahexacyclo[7.7.2.12,5.01,10.03, 8.013,17]nonadecan-8-yl] acetate · 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1001 | 0.86 | 0.86 | 81 | 966 |
| 2 | 476 | 0.73 | 0.82 | 63 | empty |
| 3 | 75 | 0.69 | 0.93 | 15 | empty |
| 4 | 413 | 0.67 | 0.80 | 52 | empty |
| 5 | 309 | 0.65 | 0.81 | 37 | empty |
Interfaces
2 interfaces between chains.
- B–D · 2102 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 409 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 7 glycan, 5 covalent (disulfide, N-glycosylation, covalent ligand).
Compared structures
- 7W77 · cryo-EM structure of human NaV1.3/beta1/beta2-bulleyaconitineA · 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 0.98
- 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 0.93
- 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 Q07699
- Every structure of UniProt O60939
- Every structure of UniProt Q9NY46
- Elsewhere: RCSB PDB 7W77 · PDBe 7W77 · UniProt Q07699 · UniProt O60939 · UniProt Q9NY46
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