Sodium-dependent serotonin transporter (SLC6A4) is a 630-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P31645.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 84.7 (confident 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 | 75% |
| 70 to 90 | Confident: backbone generally right | 10% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 14% |
What pLDDT means and how to read it
Serotonin transporter that cotransports serotonin with one Na(+) ion in exchange for one K(+) ion and possibly one proton in an overall electroneutral transport cycle. Transports serotonin across the plasma membrane from the extracellular compartment to the cytosol thus limiting serotonin intercellular signaling (PubMed:10407194, PubMed:12869649, PubMed:21730057, PubMed:27049939, PubMed:27756841, PubMed:34851672). Essential for serotonin homeostasis in the central nervous system. In the developing somatosensory cortex, acts in glutamatergic neurons to control serotonin uptake and its trophic functions accounting for proper spatial organization of cortical neurons and elaboration of sensory…
Monomer or homooligomer (By similarity). Interacts with TGFB1I1 (PubMed:16803896). Interacts with SEC23A, SEC24C and PATJ. Interacts with NOS1; the interaction may diminish the cell surface localization of SERT in the brain and, correspondingly, reduce serotonin reuptake. Interacts with filamentous actin and STX1A (By similarity). Interacts (via the N-terminus) with STX1A (via the H3 domain);…
Cell membrane, Endomembrane system, Endosome membrane, Synapse, Cell junction, focal adhesion, Cell projection, neuron projection
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9HCO | EM | 2.78 Å | A=1-630 |
| 7TXT | EM | 3.0 Å | S=77-617 |
| 5I6X | X-ray | 3.14 Å | A=76-618 |
| 5I71 | X-ray | 3.15 Å | A=76-618 |
| 5I73 | X-ray | 3.24 Å | A=76-618 |
| 9IY7 | EM | 3.27 Å | A=1-630 |
| 6VRH | EM | 3.3 Å | A=1-630 |
| 7LIA | EM | 3.3 Å | A=79-617 |
| 5I74 | X-ray | 3.4 Å | A=76-618 |
| 9PNS | EM | 3.4 Å | A=77-617 |
| 5I75 | X-ray | 3.49 Å | A=76-618 |
| 7LI6 | EM | 3.5 Å | A=79-617 |
| 7MGW | EM | 3.5 Å | A=79-615 |
| 6AWO | X-ray | 3.53 Å | A=76-618 |
| 6DZZ | EM | 3.6 Å | A=78-617 |
| 6AWN | X-ray | 3.62 Å | A=76-618 |
| 7LWD | EM | 3.65 Å | A=77-617 |
| 6AWP | X-ray | 3.8 Å | A=76-618 |
| 6VRL | EM | 3.8 Å | A=1-630 |
| 7LI8 | EM | 3.9 Å | A=79-617 |
Showing 20 of 30 experimental structures (best resolution first).
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.