DNA damage-binding protein 2 (ddb2) is a 496-residue protein from Danio rerio. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q2YDS1.
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The mean pLDDT of this model is 78.3 (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 | 63% |
| 70 to 90 | Confident: backbone generally right | 9% |
| 50 to 70 | Low: treat with caution | 3% |
| Below 50 | Very low: often disordered regions | 26% |
What pLDDT means and how to read it
Protein, which is both involved in DNA repair and protein ubiquitination, as part of the UV-DDB complex and DCX (DDB1-CUL4-X-box) complexes, respectively. Core component of the UV-DDB complex (UV-damaged DNA-binding protein complex), a complex that recognizes UV-induced DNA damage and recruit proteins of the nucleotide excision repair pathway (the NER pathway) to initiate DNA repair. The UV-DDB complex preferentially binds to cyclobutane pyrimidine dimers (CPD), 6-4 photoproducts (6-4 PP), apurinic sites and short mismatches. Also functions as the substrate recognition module for the DCX (DDB2-CUL4-X-box) E3 ubiquitin-protein ligase complex DDB2-CUL4-ROC1 (also known as CUL4-DDB-ROC1 and…
Component of the UV-DDB complex which includes ddb1 and ddb2 (PubMed:19109893). Component of a DCX (DDB1-CUL4-X-box) E3 ubiquitin-protein ligase complex that includes cul4a, or cul4b, ddb1, ddb2 and rbx1 (PubMed:22118460). A large number of other DCX complexes may also exist in which an alternate substrate targeting subunit replaces ddb2. These targeting subunits are generally known as DCAF…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3EI3 | X-ray | 2.3 Å | B=60-423 |
| 3EI2 | X-ray | 2.6 Å | B=60-423 |
| 3EI1 | X-ray | 2.8 Å | B=60-423 |
| 4A08 | X-ray | 3.0 Å | B=60-423 |
| 4A09 | X-ray | 3.1 Å | B=60-423 |
| 4A0A | X-ray | 3.6 Å | B=60-423 |
| 4A0B | X-ray | 3.8 Å | B/D=60-423 |
| 4A0K | X-ray | 5.93 Å | D=60-423 |
| 4A0L | X-ray | 7.4 Å | B/D=60-423 |
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