Lysine-specific demethylase 2A (KDM2A) is a 1162-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q9Y2K7.
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The mean pLDDT of this model is 73.3 (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 | 48% |
| 70 to 90 | Confident: backbone generally right | 17% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 31% |
What pLDDT means and how to read it
Histone demethylase that specifically demethylates 'Lys-36' of histone H3, thereby playing a central role in histone code. Preferentially demethylates dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36'. May also recognize and bind to some phosphorylated proteins and promote their ubiquitination and degradation. Required to maintain the heterochromatic state. Associates with centromeres and represses transcription of small non-coding RNAs that are encoded by the clusters of satellite repeats at the centromere. Required to sustain centromeric integrity and genomic stability, particularly during mitosis. Regulates circadian gene…
Interacts with CBX5/HP1A; the interaction promotes CBX5 localization to chromatin (PubMed:19001877). The SKP1-KDM2A complex interacts with UBB (PubMed:30033217). Part of a SCF (SKP1-cullin-F-box) protein ligase complex (PubMed:30033217)
Nucleus, nucleoplasm, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4BBQ | X-ray | 2.24 Å | A/B=567-681 |
| 6BYH | X-ray | 2.61 Å | E/F/I=888-932 |
| 2YU1 | X-ray | 2.7 Å | A=1-517 |
| 2YU2 | X-ray | 2.7 Å | A=1-517 |
| 7UV9 | EM | 3.2 Å | K=2-685 |
| 6C16 | X-ray | 3.27 Å | C/F=888-932 |
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