Crystal structure of rat vitamin D receptor bound to adamantyl vitamin D analogs: structural basis for vitamin D receptor antagonism AND/OR partial agonism

Structure

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

Ligands and binding sites

• TT2 · (1R,3R,7E,17beta)-17-{(1S,2E,5R)-5-hydroxy-1-methyl-5-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-yl]pent-2-en-1-yl}-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol · ligand · chains A
• FMT · Formic acid · additive · chains A
• EDO · 1,2-ethanediol · additive · 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–C · 531 Ų buried · 5 hydrogen bonds · protein-protein

Compared structures

• 2ZMI · Crystal Structure of Rat Vitamin D Receptor Bound to Adamantyl Vitamin D Analogs… · 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
• A1L0Z0 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain C against A, TM-score 0.61

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 A1L0Z0
• Elsewhere: RCSB PDB 2ZMI · PDBe 2ZMI · UniProt P13053 · UniProt A1L0Z0