Structure of zvdr lbd-calcitriol in complex with chimera 11

Structure

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

Ligands and binding sites

• VDX · 5-{2-[1-(5-hydroxy-1,5-dimethyl-hexyl)-7A-methyl-octahydro-inden-4-ylidene]-ethylidene}-4-methylene-cyclohexane-1,3-diol · ligand · chains A
• URL · [(2~{S})-2-azanyl-4-methyl-pentyl]carbamic acid · ligand · chains A, B
• UIL · [(2~{R})-1-azanyl-4-methyl-pentan-2-yl]carbamic acid · ligand · chains A, B
• ACT · Acetate ion · additive · chains A

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

Pockets

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

Interfaces

1 interface between chains.

• A–B · 379 Ų buried · 7 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent, 1 modified (covalent ligand, nonstandard).

Compared structures

• 6XZI · Structure of zVDR LBD-calcitriol in complex with chimera 11 · the same entry in another collection · chain A against A, TM-score 1.00
• Q9PTN2 · AlphaFold monomer V2.0 prediction for vitamin D3 receptor a (Q9PTN2) · a predicted model of the same protein · chain A 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 Q9PTN2
• Elsewhere: RCSB PDB 6XZI · PDBe 6XZI · UniProt Q9PTN2