Crystal structure of vdr-lbd complexed with an antagonist, 2- methylidene-19,26,27-trinor-22-(S)-butyl-1-hydroxy-25-oxo-25-(1H- pyrrol-2-yl)- vitamin D3

Structure

x-ray diffraction · 2 distinct chains · 65% helix, 3% strand (DSSP).

Ligands and binding sites

• 8FF · (4~{S})-4-[(1~{R})-1-[(1~{R},3~{A}~{S},4~{E}, 7~{A}~{R})-7~{A}-methyl-4-[2-[(3~{R},5~{R})-4-methylidene-3,5-bis(oxidanyl) cyclohexylidene]ethylidene]-2,3,3~{A},5,6,7-hexahydro-1~{H}-inden-1-yl]ethyl]-1-(1~{H}-pyrrol-2-yl)octan-1-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 · 550 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 5XUQ · Crystal structure of VDR-LBD complexed with an antagonist… · 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 0.79

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 5XUQ · PDBe 5XUQ · UniProt P13053 · UniProt Q15648