Crystal structure of vdr-lbd complexed with 22S-butyl-25RS- (hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1- hydroxyvitamin D3

Structure

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

Ligands and binding sites

• 8C0 · (1~{R},3~{R})-5-[(2~{E})-2-[(1~{R},3~{A}~{S}, 7~{A}~{R})-1-[(2~{R},3~{S})-3-[(3~{S})-3-(4-hydroxyphenyl)-3-methoxy-propyl]heptan-2-yl]-7~{A}-methyl-2,3,3~{A},5,6,7-hexahydro-1~{H}-inden-4-ylidene]ethylidene]-2-methylidene-cyclohexane-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 · 560 Ų buried · 6 hydrogen bonds · protein-protein

Compared structures

• 5XPM · Crystal structure of VDR-LBD complexed with 22S-Butyl-25RS-(hydroxyphenyl)-25-methoxy-2-me… · the same entry in another collection · chain A against A, TM-score 1.00
• 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 0.66

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 5XPM · PDBe 5XPM · UniProt P13053 · UniProt Q15648