Serine hydroxymethyltransferase, mitochondrial (SHMT2) is a 504-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P34897.
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The mean pLDDT of this model is 93.3 (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 | 90% |
| 70 to 90 | Confident: backbone generally right | 2% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 7% |
What pLDDT means and how to read it
Catalyzes the cleavage of serine to glycine accompanied with the production of 5,10-methylenetetrahydrofolate, an essential intermediate for purine biosynthesis (PubMed:24075985, PubMed:25619277, PubMed:29364879, PubMed:33015733). Serine provides the major source of folate one-carbon in cells by catalyzing the transfer of one carbon from serine to tetrahydrofolate (PubMed:25619277). Contributes to the de novo mitochondrial thymidylate biosynthesis pathway via its role in glycine and tetrahydrofolate metabolism: thymidylate biosynthesis is required to prevent uracil accumulation in mtDNA (PubMed:21876188). Also required for mitochondrial translation by producing…
Homotetramer; in the presence of bound pyridoxal 5'-phosphate (PubMed:25619277, PubMed:29180469). Homodimer; in the absence of bound pyridoxal 5'-phosphate (PubMed:25619277, PubMed:29180469). Pyridoxal 5'-phosphate binding mediates an important conformation change that is required for tetramerization (PubMed:25619277). Interacts with ABRAXAS2; the interaction is direct. Identified in a complex…
Mitochondrion, Mitochondrion matrix, mitochondrion nucleoid, Mitochondrion inner membrane, Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8AQL | X-ray | 1.23 Å | A/B/C/D=29-504 |
| 9RWD | X-ray | 1.3 Å | A/B/C/D=29-504 |
| 6DK3 | X-ray | 2.04 Å | A=17-504 |
| 9BOX | X-ray | 2.1 Å | A/B/C/D=43-504 |
| 6QVL | X-ray | 2.28 Å | A/B=1-504 |
| 6M5O | X-ray | 2.3 Å | A/B=17-504 |
| 6QVG | X-ray | 2.32 Å | A/B=1-504 |
| 8GKW | X-ray | 2.38 Å | A/B=29-504 |
| 5V7I | X-ray | 2.47 Å | A/B=29-504 |
| 8FJT | X-ray | 2.47 Å | A/B=29-504 |
| 8SSJ | X-ray | 2.5 Å | A/B=37-504 |
| 8FJU | X-ray | 2.51 Å | A/B=29-504 |
| 4PVF | X-ray | 2.6 Å | A/B=22-504 |
| 8GKT | X-ray | 2.64 Å | A/B=29-504 |
| 8T4O | X-ray | 2.68 Å | A/B=29-504 |
| 8TLC | X-ray | 2.72 Å | A/B=29-504 |
| 8GKZ | X-ray | 2.75 Å | A/B=29-504 |
| 7BYI | X-ray | 2.76 Å | A/B=22-504 |
| 8GKY | X-ray | 2.77 Å | A/B=29-504 |
| 8T4P | X-ray | 2.8 Å | A/B=29-504 |
Showing 20 of 27 experimental structures (best resolution first).
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