Lysine-specific histone demethylase 2 (KDM1B) is a 822-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q8NB78.
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The mean pLDDT of this model is 91.3 (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 | 87% |
| 70 to 90 | Confident: backbone generally right | 2% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 8% |
What pLDDT means and how to read it
Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated 'Lys-4' of histone H3. Has no effect on tri-methylated 'Lys-4', mono-, di- or tri-methylated 'Lys-9', mono-, di- or tri-methylated 'Lys-27', mono-, di- or tri-methylated 'Lys-36' of histone H3, or on mono-, di- or tri-methylated 'Lys-20' of histone H4. Alone, it is unable to demethylate H3K4me on nucleosomes…
Interacts with its cofactor GLYR1 at nucleosomes; this interaction stimulates H3K4me1 and H3K4me2 demethylation (PubMed:23260659, PubMed:30970244). In contrast to KDM1A, does not form a complex with RCOR1/CoREST (Probable). Possible accessory component of the polycomb repressive deubiquitinase (PR-DUB) complex, at least composed of BAP1, one of ASXL1, ASXL2 or (probably) ASXL3 and one of MBD5 or…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4HSU | X-ray | 1.99 Å | A=51-822 |
| 4GUT | X-ray | 2.0 Å | A=51-822 |
| 7XE2 | X-ray | 2.05 Å | A/B=30-822 |
| 7XE1 | X-ray | 2.07 Å | A/B=30-822 |
| 4FWE | X-ray | 2.13 Å | A=30-822 |
| 4GUS | X-ray | 2.23 Å | A=51-822 |
| 4GUU | X-ray | 2.3 Å | A=51-822 |
| 4GUR | X-ray | 2.51 Å | A=51-822 |
| 4FWF | X-ray | 2.7 Å | A=30-822 |
| 7XE3 | X-ray | 2.82 Å | A/B=30-822 |
| 4FWJ | X-ray | 2.9 Å | A/B=30-822 |
| 4GU1 | X-ray | 2.94 Å | A/B=51-822 |
| 4GU0 | X-ray | 3.1 Å | A/B/C/D=51-822 |
| 6R1U | EM | 4.36 Å | K=51-822 |
| 6R25 | EM | 4.61 Å | K=51-822 |
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