Lysine-specific demethylase 6B (Kdm6b) is a 1641-residue protein from Mus musculus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q5NCY0.
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The mean pLDDT of this model is 57.0 (low 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 | 28% |
| 70 to 90 | Confident: backbone generally right | 7% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 59% |
What pLDDT means and how to read it
Histone demethylase that specifically demethylates 'Lys-27' of histone H3, thereby playing a central role in histone code. Demethylates trimethylated and dimethylated H3 'Lys-27'. Plays a central role in regulation of posterior development, by regulating HOX gene expression. Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation (PubMed:17825402). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression by acting as a link between T-box factors and the SMARCA4-containing SWI/SNF remodeling complex (PubMed:21095589)
Interacts with TLE1 (PubMed:21095589). Component of the MLL4 complex, at least composed of KMT2B/MLL4, ASH2L, RBBP5, WDR5, and KDM6B (By similarity). Interacts with TBX21, SMARCA4, SMARCC1 and SMARCC2 (PubMed:21095589)
Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4EYU | X-ray | 2.3 Å | A/B=1155-1641 |
| 4EZH | X-ray | 2.52 Å | A/B=1155-1641 |
| 4EZ4 | X-ray | 2.99 Å | A/B=1155-1641 |
| 9NQU | EM | 3.16 Å | K=1130-1641 |
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