Research workbench
Navms voltage-gated sodium channal pore and C-terminal domain soaked with silver nitrate
Analyse Navms voltage-gated sodium channal pore and C-terminal domain soaked with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4X89
- Type
- protein
- Length
- 364 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ion transport protein
- UniProt
- A0L5S6
- Ligands
- 2CV, NA, AG
- Pockets
- 3 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 80% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 92 | 80% helix, 0% strand | A0L5S6 |
| B | Ion transport protein | protein | 90 | 80% helix, 0% strand | A0L5S6 |
| C, D | Ion transport protein | protein | 91 | 79% helix, 0% strand | A0L5S6 |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 7 copies · chains A, B, C, D
- AG · Silver ion · metal · chains B, C
- 1PE · Pentaethylene glycol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 473 | 0.66 | 0.78 | 46 | AG |
| 2 | 178 | 0.56 | 0.79 | 26 | empty |
| 3 | 216 | 0.54 | 0.77 | 31 | 2CV |
Interfaces
5 interfaces between chains.
- A–B · 714 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 699 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 201 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 141 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 46 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4X89 · NavMs voltage-gated sodium channal pore and C-terminal domain soaked with Silver nitrate · 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 A0L5S6
- Elsewhere: RCSB PDB 4X89 · PDBe 4X89 · UniProt A0L5S6
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