ATP-dependent DNA helicase DDM1 (DDM1) is a 764-residue protein from Arabidopsis thaliana. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9XFH4.
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The mean pLDDT of this model is 67.7 (low 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 | 12% |
| 70 to 90 | Confident: backbone generally right | 44% |
| 50 to 70 | Low: treat with caution | 19% |
| Below 50 | Very low: often disordered regions | 25% |
What pLDDT means and how to read it
DNA- or chromatin-stimulated ATPase that plays a role in formation, organization, stability and heritability of heterochromatin and thus regulates several physiological traits. Binds to the nucleosome and promotes chromatin remodeling in an ATP-dependent manner; induces nucleosome repositioning on a short DNA fragment, and, possibly, could be guided to target sites (including silent transposable elements) by small interfering RNAs (siRNAs). Can bind both free and nucleosomal DNA. Required for the heritable maintenance of genome integrity and transcriptional gene silencing (TGS), including homology-dependent gene silencing (HDG silencing), via the maintenance of DNA methylation (mostly on…
Interacts with the MBD domains of MBD2, MBD5 and MBD6
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8KCC | EM | 3.1 Å | K=1-764 |
| 8KCB | EM | 3.17 Å | K=1-764 |
| 7UX9 | EM | 3.2 Å | P=1-764 |
| 8WH9 | EM | 3.31 Å | K=1-764 |
| 8SKZ | EM | 3.5 Å | A=1-764 |
| 8WH5 | EM | 3.58 Å | K=1-764 |
| 8WH8 | EM | 3.6 Å | K=1-764 |
| 8WHA | EM | 4.05 Å | K/L=1-764 |
| 8J90 | EM | 4.71 Å | K=1-764 |
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