Serine hydroxymethyltransferase, cytosolic (SHMT1) is a 483-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P34896.
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The mean pLDDT of this model is 96.6 (very high 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 | 95% |
| 70 to 90 | Confident: backbone generally right | 3% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 1% |
What pLDDT means and how to read it
Pyridoxal phosphate (PLP)-dependent enzyme that catalyzes the reversible conversion of serine and tetrahydrofolate (THF) to glycine and 5,10-methylene THF, serving as a critical component of the folate cycle and facilitating one-carbon biosynthetic reactions essential for methionine, purine, and pyrimidine synthesis (PubMed:24698160, PubMed:30035852, PubMed:38996576). While its central activity involves serine cleavage, the detailed catalytic mechanisms remain under study, including both retro-aldol cleavage of the PLP-serine C(alpha)-C(beta) bond followed by formaldehyde condensation with THF, and alternative nucleophilic displacement mechanisms of the C(alpha) atom of PLP-serine aldimine…
Homotetramer comprising two obligate dimers (PubMed:24698160, PubMed:25619277, PubMed:30035852, PubMed:38996576, PubMed:9753690). Identified in complex with ABRAXAS2 and the other subunits of the BRISC complex, at least composed of ABRAXAS2, BRCC3/BRCC36, BABAM2 and BABAM1/NBA1 (PubMed:24075985). Part of the de novo thymidylate synthesis complex composed at least by SHMT1, DHFR and TYMS…
Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 7RJP | X-ray | 1.25 Å | B=270-275 |
| 7RJL | X-ray | 1.5 Å | C/D=270-275 |
| 1BJ4 | X-ray | 2.65 Å | A=11-480 |
| 6M5W | X-ray | 3.1 Å | A=1-483 |
| 8R7H | EM | 3.29 Å | A/B/C/D=1-483 |
| 8XND | X-ray | 3.45 Å | A/B/C/D=11-480 |
| 8A11 | EM | 3.52 Å | A/B/C/D=1-483 |
| 6FL5 | X-ray | 3.6 Å | A/D/G/J=11-481 |
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