Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of drip 205

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 3% strand (DSSP).

Ligands and binding sites

• YR4 · (2R)-2-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}butane-1,4-diol · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Interfaces

1 interface between chains.

• A–B · 448 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 3AUN · Crystal structure of the rat vitamin D receptor ligand binding domain complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
• P13053 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P13053) · a predicted model of the same protein · chain A against A, TM-score 0.98
• Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain B against A, TM-score 0.76

Analyse

• Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
• Every structure of UniProt P13053
• Every structure of UniProt Q15648
• Elsewhere: RCSB PDB 3AUN · PDBe 3AUN · UniProt P13053 · UniProt Q15648