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Crystal structure of navrh, a voltage-gated sodium channel
Analyse Crystal structure of navrh, a voltage-gated sodium channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DXW
- Type
- protein
- Length
- 830 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- D0RMU8
- Ligands
- BNG, PX4, CA
- Pockets
- 18 · best druggability 0.67
Structure
x-ray diffraction · 4 distinct chains · 75% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 210 | 72% helix, 0% strand | D0RMU8 |
| B | Ion transport protein | protein | 222 | 74% helix, 0% strand | D0RMU8 |
| C | Ion transport protein | protein | 199 | 80% helix, 0% strand | D0RMU8 |
| D | Ion transport protein | protein | 199 | 74% helix, 0% strand | D0RMU8 |
Ligands and binding sites
- BNG · nonyl beta-D-glucopyranoside · ligand · 4 copies · chains A, B, D, C
- PX4 · 1,2-dimyristoyl-sn-glycero-3-phosphocholine · ligand · chains A, B, C
- CA · Calcium ion · metal · 2 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 165 | 0.67 | 0.86 | 29 | PX4 |
| 2 | 159 | 0.65 | 0.85 | 29 | empty |
| 3 | 149 | 0.64 | 0.85 | 24 | empty |
| 4 | 139 | 0.64 | 0.86 | 28 | BNG |
| 5 | 142 | 0.60 | 0.83 | 17 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1722 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 1711 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1702 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1560 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4DXW · Crystal structure of NavRh, a voltage-gated sodium channel · 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 D0RMU8
- Elsewhere: RCSB PDB 4DXW · PDBe 4DXW · UniProt D0RMU8
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