Lysine-specific demethylase 2A (Kdm2a) is a 1161-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P59997.
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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 | 3% |
| Below 50 | Very low: often disordered regions | 32% |
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 (PubMed:32584788). 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 (By similarity).…
Part of a SCF (SKP1-cullin-F-box) protein ligase complex. Interacts with CBX5/HP1A; the interaction promotes CBX5 localization to chromatin (By similarity). The SKP1-KDM2A complex interacts with UBB (By similarity)
Nucleus, nucleoplasm, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4QXB | X-ray | 1.6 Å | A/C=36-364, B/D=450-517 |
| 4QX8 | X-ray | 1.65 Å | A/C=36-364, B/D=450-517 |
| 4QXC | X-ray | 1.75 Å | A/C=36-364, B/D=450-517 |
| 7UVA | X-ray | 1.98 Å | A/D=36-364, B/E=450-517 |
| 4QWN | X-ray | 2.1 Å | A/C=36-364, B/D=450-517 |
| 4QXH | X-ray | 2.2 Å | A/C=36-364, B/D=450-517 |
| 4TN7 | X-ray | 2.2 Å | A/C=36-364, B/D=450-517 |
| 4QX7 | X-ray | 2.34 Å | A/C=36-364, B/D=450-517 |
| 9WSR | EM | 2.79 Å | B=889-1161 |
| 9WSQ | EM | 3.35 Å | B/E=234-993 |
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