Histone H3 (His3) is a 136-residue protein from Drosophila melanogaster. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P02299.
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The mean pLDDT of this model is 86.4 (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 | 68% |
| 70 to 90 | Confident: backbone generally right | 5% |
| 50 to 70 | Low: treat with caution | 25% |
| Below 50 | Very low: often disordered regions | 2% |
What pLDDT means and how to read it
Core component of nucleosome. Nucleosomes wrap and compact DNA into chromatin, limiting DNA accessibility to the cellular machineries which require DNA as a template. Histones thereby play a central role in transcription regulation, DNA repair, DNA replication and chromosomal stability. DNA accessibility is regulated via a complex set of post-translational modifications of histones, also called histone code, and nucleosome remodeling. Involved in recruitment of Parp1 to chromatin and regulates its activity; inhibits DNA-dependent activation of Parp1 but contributes to nucleosome-dependent activation of Parp1 (PubMed:17827147)
The nucleosome is a histone octamer containing two molecules each of H2A, H2B, H3 and H4 assembled in one H3-H4 heterotetramer and two H2A-H2B heterodimers. The octamer wraps approximately 147 bp of DNA. Interacts (via N-terminus di- or tri-methylated on Lys-10 (H3K9me2/3)) with rhi (via Chromo domain); this interaction is direct (PubMed:24906153, PubMed:25085419). Interacts with Nasp…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6AT0 | X-ray | 1.28 Å | P=6-11 |
| 6MHA | X-ray | 1.5 Å | B=6-11 |
| 6ASZ | X-ray | 1.52 Å | P=6-11 |
| 7VRF | X-ray | 1.7 Å | C/D=5-15 |
| 4U68 | X-ray | 1.8 Å | D/E/F=5-15 |
| 1KNA | X-ray | 2.1 Å | P=2-17 |
| 9ZQB | EM | 2.1 Å | E/F=1-136 |
| 2NQB | X-ray | 2.3 Å | A/E=2-136 |
| 9ZQC | EM | 2.37 Å | E/F=1-136 |
| 1KNE | X-ray | 2.4 Å | P=2-17 |
| 2PYO | X-ray | 2.43 Å | A/E=2-136 |
| 4QUF | X-ray | 2.5 Å | P/Q/R/T/U/V=2-16 |
| 8UX1 | EM | 2.5 Å | A/E=1-136 |
| 2YBA | X-ray | 2.55 Å | C/D=2-20 |
| 4UUZ | X-ray | 2.9 Å | A=1-136 |
| 8PP7 | EM | 2.91 Å | A/E=2-136 |
| 6DZT | EM | 2.99 Å | A/E=1-136 |
| 8PP6 | EM | 3.18 Å | A/E=2-136 |
| 9ZQA | EM | 3.28 Å | E/F=1-136 |
| 9MU4 | EM | 3.29 Å | a/e=37-136 |
Showing 20 of 31 experimental structures (best resolution first).
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