Histone H2A type 1 is a 130-residue protein from Xenopus laevis. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P06897.
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The mean pLDDT of this model is 90.4 (very high 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 | 79% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 15% |
| Below 50 | Very low: often disordered regions | 0% |
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
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
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6W4L | X-ray | 1.31 Å | A=14-105 |
| 8ZVY | X-ray | 1.72 Å | A/B=14-105 |
| 1KX5 | X-ray | 1.94 Å | C/G=2-130 |
| 1KX3 | X-ray | 2.0 Å | C/G=2-130 |
| 1S32 | X-ray | 2.05 Å | C/G=2-120 |
| 3UTA | X-ray | 2.07 Å | C/G=2-130 |
| 3C1B | X-ray | 2.2 Å | C/G=2-130 |
| 3UT9 | X-ray | 2.2 Å | C/G=2-130 |
| 3UTB | X-ray | 2.2 Å | C/G=2-130 |
| 6WZ5 | EM | 2.2 Å | C/G=2-130 |
| 1M19 | X-ray | 2.3 Å | C/G=2-130 |
| 1P3I | X-ray | 2.3 Å | C/G=2-130 |
| 7TN2 | EM | 2.3 Å | C/G=2-130 |
| 9F0O | EM | 2.3 Å | C/G=11-120 |
| 9JNP | EM | 2.3 Å | C/G=2-130 |
| 5OMX | X-ray | 2.32 Å | C/G=2-130 |
| 4J8U | X-ray | 2.38 Å | C/G=2-130 |
| 1P3L | X-ray | 2.4 Å | C/G=2-130 |
| 4XZQ | X-ray | 2.4 Å | C/G=15-121 |
| 4J8W | X-ray | 2.41 Å | C/G=2-130 |
Showing 20 of 301 experimental structures (best resolution first).
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