Crystal structure of vdr-lbd complexed with 22S-butyl-2-methylidene- 19-nor-1A,25-dihydroxyvitamin D3

Structure

x-ray diffraction · 2 distinct chains · 67% helix, 3% strand (DSSP).

Ligands and binding sites

• YS9 · (1R,3R,7E,17beta)-17-[(2R,3S)-3-butyl-6-hydroxy-6-methylheptan-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

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

Interfaces

1 interface between chains.

• A–C · 560 Ų buried · 7 hydrogen bonds · protein-protein

Compared structures

• 3WTQ · Crystal structure of VDR-LBD complexed with 22S-butyl-2-methylidene-19-nor-1a,25-dihydroxy… · 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 0.65

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 3WTQ · PDBe 3WTQ · UniProt P13053 · UniProt Q15648