DNA (cytosine-5)-methyltransferase 3B (DNMT3B) is a 853-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9UBC3.
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The mean pLDDT of this model is 72.6 (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 | 48% |
| 70 to 90 | Confident: backbone generally right | 18% |
| 50 to 70 | Low: treat with caution | 2% |
| 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. DNA methylation is coordinated with methylation of histones. May preferentially methylates nucleosomal DNA within the nucleosome core region. May function as transcriptional co-repressor by associating with CBX4 and independently of DNA methylation. Seems to be involved in gene silencing (By similarity). In association with DNMT1 and via the recruitment of CTCFL/BORIS, involved in activation of BAG1 gene expression by modulating dimethylation of promoter histone H3 at H3K4 and H3K9. Isoforms 4 and 5 are probably not functional due to the deletion of two…
Interacts with BAZ2A/TIP5, SUV39H1 and CBX4. Interacts with UHRF1 (By similarity). Interacts with DNMT1 and DNMT3A, SETDB1, UBL1, UBE2I9 and ZHX1. Interacts with the PRC2/EED-EZH2 complex
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 5NRR | X-ray | 1.7 Å | A/B=206-355 |
| 3FLG | X-ray | 1.8 Å | A=206-355 |
| 5NV2 | X-ray | 2.03 Å | A/B=206-355 |
| 3QKJ | X-ray | 2.04 Å | A/B/C/D=206-355 |
| 5NRV | X-ray | 2.08 Å | A/D=206-355 |
| 7O45 | X-ray | 2.1 Å | A/B/C/D=412-554 |
| 5CIU | X-ray | 2.24 Å | A/B=206-355 |
| 6R3E | X-ray | 2.27 Å | A/B=215-351 |
| 5NR3 | X-ray | 2.3 Å | A/B=206-355 |
| 5NRS | X-ray | 2.3 Å | A/B=206-355 |
| 5NV0 | X-ray | 2.4 Å | A/B=206-355 |
| 5NVO | X-ray | 2.4 Å | A/B=206-355 |
| 5NV7 | X-ray | 2.57 Å | A/B=206-355 |
| 8ZLK | X-ray | 2.74 Å | A/B=206-355 |
| 6KDB | X-ray | 2.86 Å | A/D=571-853 |
| 6KDT | X-ray | 2.87 Å | A/D=571-853 |
| 6KDA | X-ray | 2.91 Å | A/D=571-853 |
| 6KDP | X-ray | 2.93 Å | A/D=571-853 |
| 6PA7 | EM | 2.94 Å | N/S=1-853 |
| 6U8W | X-ray | 2.95 Å | A/D=563-853 |
Showing 20 of 47 experimental structures (best resolution first).
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