Histone deacetylase RPD3 (RPD3) is a 433-residue protein from Saccharomyces cerevisiae (strain ATCC 204508 / S288c). This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P32561.
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The mean pLDDT of this model is 91.6 (very high 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 | 86% |
| 70 to 90 | Confident: backbone generally right | 3% |
| 50 to 70 | Low: treat with caution | 5% |
| Below 50 | Very low: often disordered regions | 6% |
What pLDDT means and how to read it
Catalytic component of the RPD3 histone deacetylase (HDAC) complexes RPD3C(L) and RPD3C(S) responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation plays an important role in transcriptional regulation, cell cycle progression, DNA damage response, osmotic stress response and developmental events. Is involved in rDNA and telomere silencing and in double strand breaks repair. Required for both full transcription repression and activation of many genes including cell type-specific genes (STE6, TY2 and HO), cell differentiation-specific genes (SPO13), genes that respond to external signals (PHO5) and TRK2. The…
Component of the RPD3C(L) complex composed of at least ASH1, CTI6, DEP1, PHO23, RPD3, RXT2, RXT3, SAP30, SDS3, SIN3, UME1 and UME6. Component of the RPD3C(S) complex composed of at least EAF3, RCO1, RPD3, SIN3, and UME1. Interacts with cyclophilins CPR1, CPR6 and CPR7, with the kinase HOG1, and with ESS1, CYC8 and HAC1
Cytoplasm, Nucleus
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 8HPO | EM | 2.6 Å | F/G=1-433 |
| 8TOF | EM | 2.8 Å | B=1-433 |
| 8KD3 | EM | 2.9 Å | A=1-433 |
| 8KD5 | EM | 2.9 Å | A=1-433 |
| 8KD4 | EM | 2.93 Å | A=1-433 |
| 8HXX | EM | 3.0 Å | L=1-433 |
| 8KD2 | EM | 3.02 Å | A=1-433 |
| 8KD6 | EM | 3.07 Å | A=1-433 |
| 8KD7 | EM | 3.09 Å | A=1-433 |
| 8HXY | EM | 3.1 Å | L=1-433 |
| 8HY0 | EM | 3.1 Å | L=1-433 |
| 7YI0 | EM | 3.2 Å | B=1-433 |
| 7YI3 | EM | 3.3 Å | B=1-433 |
| 8W9C | EM | 3.3 Å | B=1-433 |
| 8IHN | EM | 3.37 Å | L=1-433 |
| 7YI2 | EM | 3.4 Å | B=1-433 |
| 8KC7 | EM | 3.46 Å | A=1-433 |
| 8GA8 | EM | 3.5 Å | B/E=1-433 |
| 8W9E | EM | 3.6 Å | B=1-433 |
| 8IHT | EM | 3.72 Å | L=1-433 |
Showing 20 of 25 experimental structures (best resolution first).
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