Lysine-specific demethylase 2B (KDM2B) is a 1336-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q8NHM5.
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The mean pLDDT of this model is 67.8 (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 | 38% |
| 70 to 90 | Confident: backbone generally right | 19% |
| 50 to 70 | Low: treat with caution | 4% |
| Below 50 | Very low: often disordered regions | 39% |
What pLDDT means and how to read it
Histone demethylase that demethylates 'Lys-4' and 'Lys-36' of histone H3, thereby playing a central role in histone code (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially demethylates trimethylated H3 'Lys-4' and dimethylated H3 'Lys-36' residue while it has weak or no activity for mono- and tri-methylated H3 'Lys-36' (PubMed:16362057, PubMed:17994099, PubMed:26237645). Preferentially binds the transcribed region of ribosomal RNA and represses the transcription of ribosomal RNA genes which inhibits cell growth and proliferation (PubMed:16362057, PubMed:17994099). May also serve as a substrate-recognition component of the SCF (SKP1-CUL1-F-box protein)-type E3 ubiquitin…
Interacts with SKP1, forming heterodimers (PubMed:27568929). The heterodimeric KDM2B-SKP1 complex interacts with the PCGF1-BCORL1 heterodimeric complex to form a homotetrameric polycomb repression complex 1 (PRC1.1) (PubMed:27568929). Directly interacts with CUL1. The SKP1-KDM2B complex interacts with UBB (PubMed:30033217)
Nucleus, nucleolus, Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4O64 | X-ray | 2.13 Å | A/B/C=607-723 |
| 8HCU | X-ray | 2.2 Å | A=1103-1336 |
| 5JH5 | X-ray | 2.55 Å | A=1059-1336 |
| 6BVA | X-ray | 2.66 Å | E/F=1060-1104 |
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