MolNFT v1 · #168141 · protein
Nachbac-NAV1.7VSDII chimera and hwtx-IV complex
6W6O: “Nachbac-NAV1.7VSDII chimera and hwtx-IV complex”. Electron microscopy, 1 ligand (POV), 20 pockets (best druggability 0.80). MolNFT v1 #168141 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6W6O
- Type
- protein
- Length
- 1,044 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nachbac-NAV1.7VSDII chimera; Huwentoxin-IV
- UniProt
- Q9KCR8, Q15858, P83303
- Ligands
- POV
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 2 distinct chains · 63% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D, F, H | Nachbac-NAV1.7VSDII chimera | protein | 226 | 73% helix, 0% strand | Q9KCR8, Q15858 |
| C, E, G, I | Huwentoxin-IV | protein | 35 | 0% helix, 17% strand | P83303 |
Ligands and binding sites
- POV · (2S)-3-(hexadecanoyloxy)-2-[(9Z)-octadec-9-enoyloxy]propyl 2-(trimethylammonio)ethyl phosphate · ligand · 12 copies · chains A, H, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 828 | 0.80 | 0.82 | 83 | empty |
| 2 | 191 | 0.63 | 0.83 | 29 | empty |
| 3 | 212 | 0.60 | 0.81 | 34 | empty |
| 4 | 175 | 0.59 | 0.82 | 31 | empty |
| 5 | 203 | 0.59 | 0.81 | 34 | empty |
Interfaces
8 interfaces between chains.
- D–F · 1655 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 1654 Ų buried · 9 hydrogen bonds · protein-protein
- F–H · 1652 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 1651 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 457 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 6W6O · NaChBac-Nav1.7VSDII chimera and HWTX-IV complex · the same entry in another collection · chain I against I, TM-score 1.00
- 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 0.84
- P83303 · AlphaFold monomer V2.0 prediction for huwentoxin-IV (P83303) · a predicted model of the same protein · chain C against A, TM-score 0.79
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 Q9KCR8
- Every structure of UniProt Q15858
- Every structure of UniProt P83303
- Elsewhere: RCSB PDB 6W6O · PDBe 6W6O · UniProt Q9KCR8 · UniProt Q15858 · UniProt P83303
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.