Covalent labeling of rvdr-lbd by turn-on fluorescent probe mediated by conjugate addition and cyclization

Structure

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

Ligands and binding sites

• YSV · (1R,3R)-5-(2-((1r,3as,7ar,e)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7A-methyloctahydro-4H-inden-4-ylidene)ethylidene)-2-methylenecyclohexane-1,3-diol · ligand · chains A
• EJO · 7-(diethylamino)chromen-2-one · ligand · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–C · 563 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

• 6JEZ · Covalent labeling of rVDR-LBD by turn-on fluorescent probe mediated by conjugate addition… · 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 0.65

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 6JEZ · PDBe 6JEZ · UniProt P13053 · UniProt Q15648