Histone-lysine N-methyltransferase SMYD3 (SMYD3) is a 428-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9H7B4.
Explore in 3D Color by confidence AlphaFold DB UniProt
The mean pLDDT of this model is 97.3 (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 | 98% |
| 70 to 90 | Confident: backbone generally right | 2% |
| 50 to 70 | Low: treat with caution | 0% |
| Below 50 | Very low: often disordered regions | 0% |
What pLDDT means and how to read it
Histone methyltransferase. Specifically methylates 'Lys-4' of histone H3, inducing di- and tri-methylation, but not monomethylation (PubMed:15235609, PubMed:22419068). Also methylates 'Lys-5' of histone H4 (PubMed:22419068). Plays an important role in transcriptional activation as a member of an RNA polymerase complex (PubMed:15235609). Binds DNA containing 5'-CCCTCC-3' or 5'-GAGGGG-3' sequences (PubMed:15235609)
Interacts with HSPCA (PubMed:15235609). Interacts with HELZ (PubMed:15235609). Interacts with POLR2A; the interaction may be indirect and may be mediated by HELZ (PubMed:15235609). Interacts with HSP90AA1; this interaction enhances SMYD3 histone-lysine N-methyltransferase (PubMed:25738358)
Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6P7Z | X-ray | 1.19 Å | A=1-428 |
| 6PAF | X-ray | 1.24 Å | A=1-428 |
| 5V37 | X-ray | 1.42 Å | A=1-428 |
| 5CCL | X-ray | 1.5 Å | A=1-428 |
| 7O2C | X-ray | 1.52 Å | A=1-428 |
| 3QWP | X-ray | 1.53 Å | A=1-428 |
| 6P6K | X-ray | 1.55 Å | A=1-428 |
| 6ZRB | X-ray | 1.55 Å | A=1-428 |
| 7O2A | X-ray | 1.57 Å | A=1-428 |
| 7QNR | X-ray | 1.57 Å | A=1-428 |
| 6O9O | X-ray | 1.59 Å | A=1-428 |
| 6P6G | X-ray | 1.59 Å | A=1-428 |
| 7BJ1 | X-ray | 1.61 Å | A=1-428 |
| 7QNU | X-ray | 1.64 Å | A=1-428 |
| 5XXJ | X-ray | 1.69 Å | A=3-425 |
| 3PDN | X-ray | 1.7 Å | A=1-428 |
| 5HQ8 | X-ray | 1.72 Å | A/B=1-428 |
| 7QLB | X-ray | 1.8 Å | A=1-428 |
| 8OWO | X-ray | 1.8 Å | A=1-428 |
| 3RU0 | X-ray | 1.85 Å | A/B=2-428 |
Showing 20 of 34 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.