Lysine-specific demethylase 5A (KDM5A) is a 1690-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P29375.
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The mean pLDDT of this model is 70.7 (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 | 27% |
| 70 to 90 | Confident: backbone generally right | 41% |
| 50 to 70 | Low: treat with caution | 8% |
| Below 50 | Very low: often disordered regions | 25% |
What pLDDT means and how to read it
Histone demethylase that specifically demethylates 'Lys-4' of histone H3, thereby playing a central role in histone code. Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Regulates specific gene transcription through DNA-binding on 5'-CCGCCC-3' motif (PubMed:18270511). May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation (PubMed:19430464). May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in…
Interacts with SUZ12; the interaction is direct (By similarity). Interacts with the viral protein-binding domain of RB1. Interacts with ESR1, MYC, MYCN and LMO2. Interacts with HDAC1; this interaction impairs histone deacetylation by HDAC1 (By similarity). Interacts with BMAL1 and CLOCK. Interacts (via PHD-type 1 zinc finger) with histone H3 unmodified at 'Lys-4' and (via PHD-type 3 zinc finger)…
Nucleus, nucleolus, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 6BGY | X-ray | 1.22 Å | A=1-588 |
| 5IVB | X-ray | 1.39 Å | A=1-588 |
| 6DQ4 | X-ray | 1.39 Å | A=1-588 |
| 5IVY | X-ray | 1.45 Å | A=1-588 |
| 6BH2 | X-ray | 1.45 Å | A=1-588 |
| 6DQ8 | X-ray | 1.46 Å | A=1-588 |
| 5IVC | X-ray | 1.57 Å | A=1-588 |
| 5IVJ | X-ray | 1.57 Å | A=1-588 |
| 6BGV | X-ray | 1.59 Å | A=1-588 |
| 6DQ6 | X-ray | 1.59 Å | A=1-588 |
| 5IW0 | X-ray | 1.63 Å | A=1-588 |
| 6BGW | X-ray | 1.64 Å | A=1-588 |
| 6BH5 | X-ray | 1.65 Å | A=1-588 |
| 5IVF | X-ray | 1.68 Å | A=1-588 |
| 6BGU | X-ray | 1.68 Å | A=1-588 |
| 5ISL | X-ray | 1.69 Å | A=1-588 |
| 6BGZ | X-ray | 1.69 Å | A=1-588 |
| 6DQE | X-ray | 1.69 Å | A=1-588 |
| 6DQF | X-ray | 1.69 Å | A=1-588 |
| 6BH3 | X-ray | 1.7 Å | A=1-588 |
Showing 20 of 46 experimental structures (best resolution first).
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