Vitamin D3 receptor (Vdr) is a 423-residue protein from Rattus norvegicus. This is its AlphaFold structure prediction, created 1 Aug 2025. UniProt accession: P13053.
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The mean pLDDT of this model is 84.3 (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 | 75% |
| 70 to 90 | Confident: backbone generally right | 6% |
| 50 to 70 | Low: treat with caution | 2% |
| Below 50 | Very low: often disordered regions | 17% |
What pLDDT means and how to read it
Nuclear receptor for calcitriol, the active form of vitamin D3 which mediates the action of this vitamin on cells (PubMed:17227670). Enters the nucleus upon vitamin D3 binding where it forms heterodimers with the retinoid X receptor/RXR (By similarity). The VDR-RXR heterodimers bind to specific response elements on DNA and activate the transcription of vitamin D3-responsive target genes (By similarity). Plays a central role in calcium homeostasis (PubMed:17227670). Also functions as a receptor for the secondary bile acid lithocholic acid (LCA) and its metabolites (By similarity)
Homodimer in the absence of bound vitamin D3 (By similarity). Heterodimer with RXRA after vitamin D3 binding (By similarity). Interacts with MED1 and NCOA6 (PubMed:10866662, PubMed:15065852, PubMed:17227670). Interacts with MED1, NCOA1, NCOA2, NCOA3 and NCOA6 coactivators, leading to a strong increase of transcription of target genes (By similarity). Interacts with the corepressor NCOR1 (By…
Nucleus, Cytoplasm
Compare the prediction with experimentally determined structures of the same protein:
| PDB ID | Method | Resolution | Chains and residues |
|---|---|---|---|
| 9VOG | X-ray | 1.43 Å | A=116-423 |
| 9M1D | X-ray | 1.44 Å | A=116-423 |
| 3VTC | X-ray | 1.5 Å | A=116-423 |
| 3VT7 | X-ray | 1.65 Å | A=116-423 |
| 9M1C | X-ray | 1.67 Å | A=116-423 |
| 9M13 | X-ray | 1.68 Å | A=116-423 |
| 2ZMI | X-ray | 1.7 Å | A=116-423 |
| 3VT3 | X-ray | 1.7 Å | A=116-423 |
| 2O4J | X-ray | 1.74 Å | A=116-423 |
| 9VOL | X-ray | 1.75 Å | A=116-423 |
| 9M1B | X-ray | 1.77 Å | A=116-423 |
| 9M1A | X-ray | 1.78 Å | A=116-423 |
| 3W0H | X-ray | 1.8 Å | A=118-420 |
| 6K5O | X-ray | 1.8 Å | A=116-419 |
| 3AUN | X-ray | 1.81 Å | A=116-423 |
| 9M17 | X-ray | 1.81 Å | A=116-423 |
| 3W0J | X-ray | 1.84 Å | A=121-420 |
| 9M12 | X-ray | 1.86 Å | A/B=116-423 |
| 5B41 | X-ray | 1.89 Å | A=116-423 |
| 1RKG | X-ray | 1.9 Å | A=116-423 |
Showing 20 of 92 experimental structures (best resolution first).
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