Research workbench
Navab voltage-gated sodium channel, I217C, in complex with class 1C anti-arrhythmic flecainide
Analyse Navab voltage-gated sodium channel, I217C, in complex with class 1C… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MVX
- Type
- protein
- Length
- 847 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- K4D, PO4
- Pockets
- 18 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 84% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 213 | 83% helix, 0% strand | A8EVM5 |
| B | Ion transport protein | protein | 211 | 84% helix, 0% strand | A8EVM5 |
| C | Ion transport protein | protein | 214 | 85% helix, 0% strand | A8EVM5 |
| D | Ion transport protein | protein | 209 | 83% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- K4D · Flecainide · ligand · chains A, B, C, D
- PO4 · Phosphate ion · ion · 10 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 747 | 0.79 | 0.83 | 103 | K4D |
| 2 | 252 | 0.67 | 0.82 | 39 | empty |
| 3 | 112 | 0.65 | 0.89 | 28 | empty |
| 4 | 63 | 0.64 | 0.93 | 24 | empty |
| 5 | 427 | 0.64 | 0.77 | 43 | empty |
Interfaces
4 interfaces between chains.
- C–D · 1483 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 1448 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1442 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 1354 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 6MVX · NavAb Voltage-gated Sodium Channel, I217C, in Complex with Class 1C Anti-arrhythmic… · the same entry in another collection · chain A against A, TM-score 1.00
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 A8EVM5
- Elsewhere: RCSB PDB 6MVX · PDBe 6MVX · UniProt A8EVM5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.