Sodium channel protein type 5 subunit alpha (Scn5a) is a 2019-residue protein from Rattus norvegicus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P15389.
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The mean pLDDT of this model is 66.8 (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 | 11% |
| 70 to 90 | Confident: backbone generally right | 47% |
| 50 to 70 | Low: treat with caution | 16% |
| Below 50 | Very low: often disordered regions | 26% |
What pLDDT means and how to read it
Pore-forming subunit of Nav1.5, a voltage-gated sodium (Nav) channel that directly mediates the depolarizing phase of action potentials in excitable membranes (By similarity). 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 (By similarity). The influx of Na(+) ions provokes membrane depolarization, initiating the propagation of electrical signals throughout cells and tissues (PubMed:24497506,…
Interact with regulatory subunit SCN1B (By similarity). May not form the same regulatory interactions with beta subunits as other Navs do (PubMed:31866066). Interacts with the PDZ domain of the syntrophin SNTA1, SNTB1 and SNTB2. Interacts with NEDD4, NEDD4L, WWP2 and GPD1L. Interacts with CALM. Interacts with FGF13; the interaction is direct and may regulate SNC5A density at membranes and…
Cell membrane, Cytoplasm, perinuclear region, Cell membrane, sarcolemma, T-tubule, Cell junction
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8F6P | EM | 3.2 Å | A=1-1898 |
| 6UZ0 | EM | 3.24 Å | A=1-1898 |
| 7K18 | EM | 3.3 Å | A=1-1898 |
| 8T6L | EM | 3.3 Å | A=1-1931 |
| 7FBS | EM | 3.4 Å | A=1-1898 |
| 7XSU | EM | 3.4 Å | A=1-1898 |
| 6UZ3 | EM | 3.5 Å | A=1-1898 |
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