MolNFT v1 · #114756 · protein
Navms voltage-gated sodium channel pore and C-terminal domain
5BZB · Ion transport protein: “Navms voltage-gated sodium channel pore and C-terminal domain”. X-ray diffraction, 2 ligands (2CV, NA), 2 pockets (best druggability 0.67). MolNFT v1 #114756 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5BZB
- 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
- Pockets
- 2 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ion transport protein | protein | 92 | 78% helix, 0% strand | A0L5S6 |
| B | Ion transport protein | protein | 90 | 80% helix, 0% strand | A0L5S6 |
| C, D | Ion transport protein | protein | 91 | 80% helix, 0% strand | A0L5S6 |
Ligands and binding sites
- 2CV · Hega-10 · ligand · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 6 copies · chains A, B, C, D
- 12P · Dodecaethylene glycol · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.67 | 0.78 | 48 | 2CV |
| 2 | 509 | 0.66 | 0.77 | 49 | 2CV |
Interfaces
5 interfaces between chains.
- A–B · 696 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 679 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 178 Ų buried · 0 hydrogen bonds · protein-protein
- B–C · 152 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 49 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5BZB · NavMs voltage-gated sodium channel pore and C-terminal domain · 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 5BZB · PDBe 5BZB · UniProt A0L5S6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.