Lysine-specific histone demethylase 1A (KDM1A) is a 852-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: O60341.
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The mean pLDDT of this model is 84.2 (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 | 76% |
| 70 to 90 | Confident: backbone generally right | 2% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 20% |
What pLDDT means and how to read it
Histone demethylase that can demethylate both 'Lys-4' (H3K4me) and 'Lys-9' (H3K9me) of histone H3, thereby acting as a coactivator or a corepressor, depending on the context (PubMed:15620353, PubMed:15811342, PubMed:16079794, PubMed:16079795, PubMed:16140033, PubMed:16223729, PubMed:27292636). Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed (PubMed:15620353, PubMed:15811342, PubMed:16079794, PubMed:21300290, PubMed:26214369). Acts as a corepressor by mediating demethylation of H3K4me, a specific tag for epigenetic transcriptional activation. Demethylates both mono- (H3K4me1) and di-methylated (H3K4me2) (PubMed:15620353,…
Component of a histone demethylase complex with RCOR1 (PubMed:16885027, PubMed:20389281, PubMed:21300290, PubMed:23721412). Component of a RCOR/GFI/KDM1A/HDAC complex (PubMed:11102443, PubMed:12032298). Component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B, KDM1A, RCOR1 and PHF21A. The BHC complex may also contain ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I (PubMed:12493763,…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6E1F | X-ray | 1.16 Å | A/B/C/D=183-267 |
| 5IT3 | X-ray | 1.4 Å | A/B=183-267 |
| 5AFW | X-ray | 1.6 Å | B=108-119 |
| 7JK7 | X-ray | 1.96 Å | A=104-129 |
| 7JJM | X-ray | 2.06 Å | A=104-129 |
| 2Z3Y | X-ray | 2.25 Å | A=172-833 |
| 2Z5U | X-ray | 2.25 Å | A=172-833 |
| 6KGO | X-ray | 2.25 Å | A=172-833 |
| 6KGP | X-ray | 2.25 Å | A=172-833 |
| 7E0G | X-ray | 2.25 Å | A=172-833 |
| 7XW8 | X-ray | 2.28 Å | A=172-833 |
| 2DW4 | X-ray | 2.3 Å | A=172-831 |
| 6KGQ | X-ray | 2.32 Å | A=172-833 |
| 6KGR | X-ray | 2.32 Å | A=172-833 |
| 7W3L | X-ray | 2.51 Å | A=172-833 |
| 5H6Q | X-ray | 2.53 Å | A=172-833 |
| 2IW5 | X-ray | 2.57 Å | A=171-836 |
| 5H6R | X-ray | 2.6 Å | A=172-833 |
| 5L3D | X-ray | 2.6 Å | A=1-852 |
| 6TUY | X-ray | 2.6 Å | A=1-852 |
Showing 20 of 128 experimental structures (best resolution first).
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