Crystal structure of vdr-lbd complexed with 22R-butyl-2-methylidene- 26,27-dimethyl-19,24-dinor-1 ,25-dihydroxyvitamin D3

Structure

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

Ligands and binding sites

• YA2 · (1R,3R,7E,17beta)-17-[(2R,3R)-3-butyl-5-ethyl-5-hydroxyheptan-2-yl]-2-methylidene-9,10-secoestra-5,7-diene-1,3-diol · ligand · chains A

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.

Interfaces

1 interface between chains.

• A–C · 554 Ų buried · 8 hydrogen bonds · protein-protein

Compared structures

• 3WT7 · Crystal structure of VDR-LBD complexed with 22R-Butyl-2-methylidene-26,27-dimethyl-19,24-d… · 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 C against A, TM-score 0.68

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 3WT7 · PDBe 3WT7 · UniProt P13053 · UniProt Q15648