Lysine-specific demethylase 4A (KDM4A) is a 1064-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O75164.
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The mean pLDDT of this model is 71.8 (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 | 42% |
| 70 to 90 | Confident: backbone generally right | 22% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 31% |
What pLDDT means and how to read it
Histone demethylase that specifically demethylates 'Lys-9' and 'Lys-36' residues of histone H3, thereby playing a central role in histone code (PubMed:16603238, PubMed:26741168, PubMed:21768309). Does not demethylate histone H3 'Lys-4', H3 'Lys-27' nor H4 'Lys-20' (PubMed:16603238, PubMed:26741168, PubMed:21768309). Demethylates trimethylated H3 'Lys-9' and H3 'Lys-36' residue, while it has no activity on mono- and dimethylated residues (PubMed:16603238, PubMed:26741168, PubMed:21768309). Demethylation of Lys residue generates formaldehyde and succinate (PubMed:16603238). Also able to demethylate histone H1-4 methylated at 'Lys-26' (H1.4K26me1, H1.4K26me2 and H1.4K26me3) (PubMed:19144645,…
Interacts with histone deacetylase proteins HDAC1, HDAC2 and HDAC3. Interacts with RB and NCOR1. Interacts with VRK1 (PubMed:37179361). Interacts with FBXO22; this interaction promotes KDM4A ubiquitination (PubMed:21768309)
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9GP4 | X-ray | 1.59 Å | A=897-1011 |
| 9GII | X-ray | 1.7 Å | A=897-1011 |
| 6G5X | X-ray | 1.78 Å | A/B=1-359 |
| 2QQR | X-ray | 1.8 Å | A/B=897-1011 |
| 4V2W | X-ray | 1.81 Å | A/B=1-359 |
| 5VAR | X-ray | 1.83 Å | A=897-1011 |
| 6G5W | X-ray | 1.83 Å | A/B=1-359 |
| 9GLE | X-ray | 1.88 Å | A/B=1-359 |
| 2OX0 | X-ray | 1.95 Å | A/B=1-359 |
| 6H8P | X-ray | 1.98 Å | A/B=1-359 |
| 2P5B | X-ray | 1.99 Å | A/B=2-350 |
| 3PDQ | X-ray | 1.99 Å | A/B=1-359 |
| 5D6W | X-ray | 1.99 Å | A/B/C/D=895-1011 |
| 2OQ6 | X-ray | 2.0 Å | A/B=1-359 |
| 2PXJ | X-ray | 2.0 Å | A/B=2-348 |
| 4V2V | X-ray | 2.0 Å | A/B=1-359 |
| 5A7Q | X-ray | 2.0 Å | A/B=1-359 |
| 5ANQ | X-ray | 2.0 Å | A/B=1-359 |
| 2YBP | X-ray | 2.02 Å | A/B=1-359 |
| 2Q8C | X-ray | 2.05 Å | A/B=1-350 |
Showing 20 of 89 experimental structures (best resolution first).
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