Sodium channel protein type 2 subunit alpha (SCN2A) is a 2005-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q99250.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 68.8 (low overall). pLDDT is AlphaFold's per-residue confidence score from 0 to 100. In MolViewer, choose the B-factor color scheme to color the model by pLDDT, because AlphaFold stores it in the B-factor column.
| pLDDT band | Meaning | Share of residues |
|---|---|---|
| Above 90 | Very high: backbone and side chains are usually accurate | 17% |
| 70 to 90 | Confident: backbone generally right | 46% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 26% |
What pLDDT means and how to read it
Mediates the voltage-dependent sodium ion permeability of excitable membranes. Assuming opened or closed conformations in response to the voltage difference across the membrane, the protein forms a sodium-selective channel through which Na(+) ions may pass in accordance with their electrochemical gradient (PubMed:1325650, PubMed:17021166, PubMed:28256214, PubMed:29844171). Implicated in the regulation of hippocampal replay occurring within sharp wave ripples (SPW-R) important for memory (By similarity)
Heterooligomer of a large alpha subunit and a smaller beta subunit. Heterooligomer with SCN2B or SCN4B; disulfide-linked. Heterooligomer with SCN1B or SCN3B; non-covalently linked. Interacts with NEDD4L. Interacts with CALM. Interacts with TMEM233 (PubMed:37117223). Interacts with the conotoxin GVIIJ (PubMed:24497506). Interacts with the spider beta/delta-theraphotoxin-Pre1a (PubMed:28428547).…
Cell membrane
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4RLY | X-ray | 2.5 Å | A=1102-1120 |
| 6J8E | EM | 3.0 Å | A=1-2005 |
| 4JPZ | X-ray | 3.02 Å | B/H=1777-1937 |
| 2KAV | NMR | A=1777-1882 | |
| 6BUT | NMR | B=1901-1927 |
MolViewer loads the AlphaFold model straight from AlphaFold DB into your browser. Show it as a cartoon, color by pLDDT, measure distances and angles, and load a PDB structure next to it to compare.