DNA (cytosine-5)-methyltransferase 3A (DNMT3A) is a 912-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9Y6K1.
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The mean pLDDT of this model is 72.9 (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 | 50% |
| 70 to 90 | Confident: backbone generally right | 14% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 32% |
What pLDDT means and how to read it
Required for genome-wide de novo methylation and is essential for the establishment of DNA methylation patterns during development (PubMed:12138111, PubMed:16357870, PubMed:30478443). DNA methylation is coordinated with methylation of histones (PubMed:12138111, PubMed:16357870, PubMed:30478443). It modifies DNA in a non-processive manner and also methylates non-CpG sites (PubMed:12138111, PubMed:16357870, PubMed:30478443). May preferentially methylate DNA linker between 2 nucleosomal cores and is inhibited by histone H1 (By similarity). Plays a role in paternal and maternal imprinting (By similarity). Required for methylation of most imprinted loci in germ cells (By similarity). Acts as a…
Heterotetramer composed of 1 DNMT3A homodimer and 2 DNMT3L subunits (DNMT3L-DNMT3A-DNMT3A-DNMT3L) (PubMed:17713477, PubMed:19834512). Interacts with UBC9, PIAS1 and PIAS2 (By similarity). Binds the ZBTB18 transcriptional repressor (By similarity). Interacts with SETDB1 (PubMed:16682412). Associates with HDAC1 through its ADD domain (By similarity). Interacts with UHRF1 (By similarity). Interacts…
Nucleus, Chromosome, Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8BA5 | X-ray | 1.45 Å | A=476-614 |
| 4QBS | X-ray | 1.8 Å | A=476-611 |
| 4QBR | X-ray | 1.9 Å | A/C=476-611 |
| 3A1B | X-ray | 2.29 Å | A=476-614 |
| 3A1A | X-ray | 2.3 Å | A=476-614 |
| 3LLR | X-ray | 2.3 Å | A/B/C/D/E=275-427 |
| 3SVM | X-ray | 2.31 Å | P=40-53 |
| 6W8B | X-ray | 2.4 Å | A/D/H/K=628-912 |
| 4QBQ | X-ray | 2.41 Å | A/C=479-610 |
| 6W8J | X-ray | 2.44 Å | A/D=628-912 |
| 8TE1 | X-ray | 2.48 Å | A/B/C/D/E/F/G/H=628-912 |
| 6W89 | X-ray | 2.5 Å | A/D/G/J=628-912 |
| 6W8D | X-ray | 2.6 Å | A/D=628-912 |
| 5YX2 | X-ray | 2.65 Å | A/D=628-912 |
| 8TE4 | X-ray | 2.65 Å | A/B/C/D/E/F/G/H=628-912 |
| 8UW1 | EM | 2.88 Å | K=159-228 |
| 2QRV | X-ray | 2.89 Å | A/D/E/H=627-912 |
| 4U7T | X-ray | 2.9 Å | A/C=476-912 |
| 6PA7 | EM | 2.94 Å | K/P=224-912 |
| 6BRR | X-ray | 2.97 Å | A/D=628-912 |
Showing 20 of 43 experimental structures (best resolution first).
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