Crystal structure of rarbeta lbd in complex with agonist BMS411 [4- {[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl) CARBONYL]AMINO}BENZOIC acid]

Structure

x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).

Ligands and binding sites

• 1NY · 4-{[(5,5-dimethyl-8-phenyl-5,6-dihydronaphthalen-2-yl)carbonyl]amino}benzoic acid · ligand · 2 copies · chains A, B
• PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · chains B
• FLC · Citrate anion · additive · chains A, G

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

Pockets

8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.

Interfaces

3 interfaces between chains.

• A–B · 1090 Ų buried · 12 hydrogen bonds · protein-protein
• A–G · 533 Ų buried · 4 hydrogen bonds · protein-protein
• B–F · 511 Ų buried · 4 hydrogen bonds · protein-protein

Compared structures

• 4JYG · Crystal structure of RARbeta LBD in complex with agonist BMS411… · the same entry in another collection · chain A against A, TM-score 1.00
• P10826 · AlphaFold monomer V2.0 prediction for retinoic acid receptor beta (P10826) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P10826
• Every structure of UniProt Q15788
• Elsewhere: RCSB PDB 4JYG · PDBe 4JYG · UniProt P10826 · UniProt Q15788