Sodium channel protein type 5 subunit alpha (SCN5A) is a 2016-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q14524.
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The mean pLDDT of this model is 67.3 (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 | 15% |
| 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 (PubMed:33712541, 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:33712541, PubMed:40768348). The influx of Na(+) ions provokes membrane depolarization, initiating the propagation of electrical signals throughout cells…
Interact with regulatory subunit SCN1B (PubMed:21994374). May not form the same regulatory interactions with beta subunits as other Navs do (By similarity). Interacts with the PDZ domain of the syntrophin SNTA1, SNTB1 and SNTB2 (By similarity). Interacts with NEDD4, NEDD4L, WWP2 and GPD1L (PubMed:15217910, PubMed:15548568, PubMed:19666841). Interacts with CALM (PubMed:21167176, PubMed:22705208,…
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 |
|---|---|---|---|
| 4DJC | X-ray | 1.35 Å | B=1491-1522 |
| 4DCK | X-ray | 2.2 Å | A=1773-1940 |
| 5DBR | X-ray | 2.25 Å | C=1483-1529 |
| 6MUD | X-ray | 2.69 Å | B=1786-1922 |
| 4OVN | X-ray | 2.8 Å | F/G/H/I/J=1773-1929 |
| 9V3S | EM | 3.0 Å | A=1-1894 |
| 6LQA | EM | 3.3 Å | B=1-2016 |
| 7DTC | EM | 3.3 Å | A=1-2016 |
| 9ITH | EM | 3.4 Å | A=1-2016 |
| 9P24 | EM | 3.48 Å | A=1-2016 |
| 8VYJ | EM | 3.6 Å | A=1-2016 |
| 4JQ0 | X-ray | 3.84 Å | D=1773-1940 |
| 8VYK | EM | 3.9 Å | A=1-2016 |
| 2KBI | NMR | A=1773-1865 | |
| 2L53 | NMR | B=1901-1927 | |
| 7L83 | NMR | A=1597-1633 |
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