Bifunctional peptidase and arginyl-hydroxylase JMJD5 (KDM8) is a 416-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: Q8N371.
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The mean pLDDT of this model is 88.9 (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 | 14% |
| 50 to 70 | Low: treat with caution | 1% |
| Below 50 | Very low: often disordered regions | 9% |
What pLDDT means and how to read it
Bifunctional enzyme that acts both as an endopeptidase and 2-oxoglutarate-dependent monooxygenase (PubMed:28847961, PubMed:28982940, PubMed:29459673, PubMed:29563586). Endopeptidase that cleaves histones N-terminal tails at the carboxyl side of methylated arginine or lysine residues, to generate 'tailless nucleosomes', which may trigger transcription elongation (PubMed:28847961, PubMed:28982940, PubMed:29459673). Preferentially recognizes and cleaves monomethylated and dimethylated arginine residues of histones H2, H3 and H4. After initial cleavage, continues to digest histones tails via its aminopeptidase activity (PubMed:28847961, PubMed:29459673). Upon DNA damage, cleaves the N-terminal…
Can form homodimers (via JmjC domain) (PubMed:24100311, PubMed:28982940). Found in a complex with RCCD1 (PubMed:24981860). Interacts (via N-terminus) with RCCD1 (via N-terminus); this interaction stimulates H3K36me3 and H3K36me2 demethylation (PubMed:24981860, PubMed:28455245). Interacts (via JmjC domain) with H3C1 (PubMed:28982940). Interacts with FBXL3 and PSMD2 (By similarity). Interacts with…
Nucleus, Chromosome
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 4GJZ | X-ray | 1.05 Å | A=183-416 |
| 6F4Q | X-ray | 1.12 Å | A=183-416 |
| 6F4T | X-ray | 1.22 Å | A=183-416 |
| 4GJY | X-ray | 1.25 Å | A=183-416 |
| 6F4O | X-ray | 1.28 Å | A=183-416 |
| 6F4R | X-ray | 1.3 Å | A=183-416 |
| 6I9N | X-ray | 1.36 Å | A=183-416 |
| 6F4P | X-ray | 1.45 Å | A=183-416 |
| 6F4S | X-ray | 1.46 Å | A=183-416 |
| 7UQ3 | X-ray | 1.49 Å | A=183-416 |
| 6I9L | X-ray | 1.53 Å | A=183-416 |
| 4QU1 | X-ray | 1.57 Å | A=183-416 |
| 7DYT | X-ray | 1.62 Å | A=183-416 |
| 6I9M | X-ray | 1.65 Å | A=183-416 |
| 6F4M | X-ray | 1.71 Å | A=183-416 |
| 7DYU | X-ray | 1.72 Å | A=183-416 |
| 7DYV | X-ray | 1.92 Å | A=183-416 |
| 6AVS | X-ray | 2.02 Å | A=183-416 |
| 7DYW | X-ray | 2.13 Å | A=183-416 |
| 6AX3 | X-ray | 2.25 Å | A=184-416 |
Showing 20 of 26 experimental structures (best resolution first).
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