Crystal structure of the human vdr ligand binding domain bound to the synthetic agonist compound 2ALPHA-methyl-AMCR277A(C23S)

Structure

x-ray diffraction · 1 distinct chain · 65% helix, 3% strand (DSSP).

Ligands and binding sites

• 2MV · (1S,2S,3R,5Z,7E,14beta,17alpha)-17-[(2S,4S)-4-(2-hydroxy-2-methylpropyl)-2-methyltetrahydrofuran-2-yl]-2-methyl-9,10-secoandrosta-5,7,10-triene-1,3-diol · ligand · chains X
• SO4 · Sulfate ion · ion · 2 copies · chains X

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

Pockets

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

Compared structures

• 3A3Z · Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist… · the same entry in another collection · chain X against X, TM-score 1.00
• P11473 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor (P11473) · a predicted model of the same protein · chain X against A, TM-score 0.94

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 P11473
• Elsewhere: RCSB PDB 3A3Z · PDBe 3A3Z · UniProt P11473