T-DNA border endonuclease VirD2 (virD2) is a 447-residue protein from Agrobacterium fabrum (strain C58 / ATCC 33970). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P18592.
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The mean pLDDT of this model is 64.6 (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 | 36% |
| 70 to 90 | Confident: backbone generally right | 11% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 51% |
What pLDDT means and how to read it
Tumor formation by A.tumefaciens involves the transfer and integration of a defined segment (T-DNA) of Ti plasmid DNA into the plant nuclear genome. The virD operon encodes a site-specific endonuclease that cleaves at a unique site within both 24 bp direct repeats flanking the T-DNA
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4BQK | X-ray | 2.0 Å | C/D=415-434 |
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