Sodium channel protein type 9 subunit alpha (SCN9A) is a 1988-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q15858.
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The mean pLDDT of this model is 69.1 (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 | 18% |
| 70 to 90 | Confident: backbone generally right | 45% |
| 50 to 70 | Low: treat with caution | 12% |
| Below 50 | Very low: often disordered regions | 25% |
What pLDDT means and how to read it
Pore-forming subunit of Nav1.7, a voltage-gated sodium (Nav) channel that directly mediates the depolarizing phase of action potentials in excitable membranes (PubMed:38381792, PubMed:40768348). Navs, also called VGSCs (voltage-gated sodium channels) or VDSCs (voltage-dependent sodium channels), operate by switching between closed and open conformations depending on the voltage difference across the membrane. In the open conformation they allow Na(+) ions to selectively pass through the pore, along their electrochemical gradient (PubMed:38381792, PubMed:40768348). The influx of Na(+) ions provokes membrane depolarization, initiating the propagation of electrical signals throughout cells…
The Nav1.7 voltage-gated sodium channel consists of an ion-conducting alpha subunit SCN9A which is functional on its own regulated by one or more beta-1 (SCN1B), beta-2 (SCN2B), beta-3 (SCN3B) and beta-4 (SCN4B) subunits (PubMed:17167479, PubMed:25240195, PubMed:30765606, PubMed:7720699, PubMed:40768348). SCN1B and SCN3B are non-covalently associated with SCN9A (PubMed:40768348). SCN2B and SCN4B…
Cell membrane, Cell projection, neuron projection, Cell projection, axon
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8YHZ | X-ray | 1.62 Å | P=764-774 |
| 7W9K | EM | 2.2 Å | A=1-1988 |
| 8F0P | EM | 2.2 Å | A=257-275, A=1501-1631 |
| 8F0Q | EM | 2.5 Å | A=257-275, A=1501-1631 |
| 8I5Y | EM | 2.6 Å | A=1-1988 |
| 21TQ | EM | 2.7 Å | A=1-1988 |
| 7XVE | EM | 2.7 Å | A=1-1988 |
| 8I5B | EM | 2.7 Å | A=1-1988 |
| 8I5G | EM | 2.7 Å | A=1-1988 |
| 8THH | EM | 2.7 Å | A=1-1988 |
| 7XVF | EM | 2.8 Å | A=1-1988 |
| 8G1A | EM | 2.8 Å | A=1-1988 |
| 8XMM | EM | 2.89 Å | A=1-1988 |
| 7W9P | EM | 2.9 Å | A=1-1988 |
| 8F0R | EM | 2.9 Å | A=257-275, A=1501-1631 |
| 8I5X | EM | 2.9 Å | A=1-1988 |
| 8S9B | EM | 2.9 Å | A=1-1988 |
| 8THG | EM | 2.9 Å | A=1-1988 |
| 9ITI | EM | 2.92 Å | A=1-1988 |
| 21TP | EM | 3.0 Å | A=1-1988 |
Showing 20 of 43 experimental structures (best resolution first).
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