Histone deacetylase 4 (HDAC4) is a 1084-residue protein from Homo sapiens. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P56524.
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The mean pLDDT of this model is 65.4 (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 | 33% |
| 70 to 90 | Confident: backbone generally right | 14% |
| 50 to 70 | Low: treat with caution | 9% |
| Below 50 | Very low: often disordered regions | 44% |
What pLDDT means and how to read it
Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Involved in muscle maturation via its interaction with the myocyte enhancer factors such as MEF2A, MEF2C and MEF2D. Involved in the MTA1-mediated epigenetic regulation of ESR1 expression in breast cancer. Deacetylates HSPA1A and HSPA1B at 'Lys-77' leading to their preferential binding to co-chaperone STUB1 (PubMed:27708256)
Homodimer. Homodimerization via its N-terminal domain (PubMed:12032081). Interacts with MEF2A (PubMed:10487761). Interacts with MEF2C and MEF2D (PubMed:10523670). Interacts with AHRR (By similarity). Interacts with NR2C1 (PubMed:11463856). Interacts with HDAC7 (By similarity). Interacts with a 14-3-3 chaperone proteins in a phosphorylation dependent manner (PubMed:10958686). Interacts with…
Nucleus, Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 3V31 | X-ray | 1.57 Å | B=343-359 |
| 2VQM | X-ray | 1.8 Å | A=648-1057 |
| 3UXG | X-ray | 1.85 Å | B=343-359 |
| 5ZOO | X-ray | 1.85 Å | G=652-1053 |
| 3UZD | X-ray | 1.86 Å | B=343-359 |
| 2VQQ | X-ray | 1.9 Å | A/B=648-1057 |
| 2VQJ | X-ray | 2.1 Å | A=648-1057 |
| 2VQO | X-ray | 2.15 Å | A/B=648-1057 |
| 6FYZ | X-ray | 2.15 Å | A/B/C=648-1033 |
| 8PDE | X-ray | 2.4 Å | C/X=167-183 |
| 2H8N | X-ray | 2.6 Å | A/B/C/D=62-153 |
| 5A2S | X-ray | 2.65 Å | A/B=648-1033 |
| 5ZOP | X-ray | 2.7 Å | G=652-1050 |
| 4CBY | X-ray | 2.72 Å | A/B/C/D=648-1033 |
| 2O94 | X-ray | 3.0 Å | A/B/C/D=62-153 |
| 2VQW | X-ray | 3.0 Å | G=648-1057 |
| 4CBT | X-ray | 3.03 Å | A/B/C=648-1033 |
| 2VQV | X-ray | 3.3 Å | A/B=648-1057 |
| 7XUZ | X-ray | 3.59 Å | A/B=62-192 |
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