MolNFT v1 · #153256 · protein
Human NAV1.2-BETA2-kiiia ternary complex
6J8E · Sodium channel subunit beta-2: “Human NAV1.2-BETA2-kiiia ternary complex”. Electron microscopy, 4 ligands (9Z9, NAG, BMA), 20 pockets (best druggability 0.80). MolNFT v1 #153256 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 6J8E
- Type
- protein
- Length
- 1,277 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sodium channel subunit beta-2; Sodium channel protein type 2 subunit alpha; Mu-conotoxin…
- UniProt
- O60939, Q99250, P0C195
- Ligands
- 9Z9, NAG, BMA, NA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 3 distinct chains · 59% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Sodium channel subunit beta-2 | protein | 122 | 5% helix, 46% strand | O60939 |
| A | Sodium channel protein type 2 subunit alpha | protein | 1139 | 65% helix, 2% strand | Q99250 |
| D | Mu-conotoxin kiiia | protein | 16 | 38% helix, 0% strand | P0C195 |
Ligands and binding sites
- 9Z9 · (3beta,14beta,17beta,25R)-3-[4-methoxy-3-(methoxymethyl)butoxy]spirost-5-en · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 360 | 0.80 | 0.90 | 56 | NA |
| 2 | 290 | 0.77 | 0.88 | 47 | 9Z9 |
| 3 | 204 | 0.74 | 0.90 | 32 | empty |
| 4 | 525 | 0.70 | 0.79 | 56 | empty |
| 5 | 503 | 0.69 | 0.80 | 57 | empty |
Interfaces
2 interfaces between chains.
- A–D · 986 Ų buried · 11 hydrogen bonds · protein-protein
- C–A · 467 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 6J8E · Human Nav1.2-beta2-KIIIA ternary complex · the same entry in another collection · chain C against C, TM-score 1.00
- O60939 · AlphaFold monomer V2.0 prediction for sodium channel subunit beta-2 (O60939) · a predicted model of the same protein · chain C against A, TM-score 0.98
- Q99250 · AlphaFold monomer V2.0 prediction for sodium channel protein type 2 subunit alpha (Q99250) · a predicted model of the same protein · chain A against A, TM-score 0.98
- P0C195 · AlphaFold monomer V2.0 prediction for mu-conotoxin kiiib (P0C195) · a predicted model of the same protein · chain D against A, TM-score 0.26
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 O60939
- Every structure of UniProt Q99250
- Every structure of UniProt P0C195
- Elsewhere: RCSB PDB 6J8E · PDBe 6J8E · UniProt O60939 · UniProt Q99250 · UniProt P0C195
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.