Research workbench
Crystal structure of the navab voltage-gated sodium channel (wild- type, 3.2 a)
Analyse Crystal structure of the navab voltage-gated sodium channel (wild- type, 3.2 a) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EKW
- Type
- protein
- Length
- 868 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A8EVM5
- Ligands
- PX4, PO4
- Pockets
- 15 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 71% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ion transport protein | protein | 219 | 70% helix, 0% strand | A8EVM5 |
| C | Ion transport protein | protein | 213 | 73% helix, 0% strand | A8EVM5 |
| D | Ion transport protein | protein | 217 | 70% helix, 0% strand | A8EVM5 |
Ligands and binding sites
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · 5 copies · chains A, B, C, D
- PO4 · Phosphate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 570 | 0.72 | 0.80 | 50 | PX4 |
| 2 | 440 | 0.70 | 0.80 | 51 | PX4 |
| 3 | 209 | 0.56 | 0.78 | 25 | empty |
| 4 | 232 | 0.50 | 0.76 | 24 | empty |
| 5 | 130 | 0.49 | 0.79 | 20 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1570 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 1436 Ų buried · 10 hydrogen bonds · protein-protein
- A–D · 272 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 1 hydrogen bond · protein-protein
- B–D · 89 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 44 modified (engineered).
Compared structures
- 4EKW · Crystal structure of the NavAb voltage-gated sodium channel (wild-type, 3.2 A) · 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 4EKW · PDBe 4EKW · UniProt A8EVM5
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.