5YSY image
Deposition Date 2017-11-16
Release Date 2018-04-11
Last Version Date 2023-11-22
Entry Detail
PDB ID:
5YSY
Keywords:
TRANSCRIPTION
Title:
Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2R,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol
Biological Source:
Source Organism:
Homo sapiens (Taxon ID: 9606)
Host Organism:
Escherichia coli
Method Details:
Experimental Method:
X-RAY DIFFRACTION
Resolution:
2.00 Å
R-Value Free:
0.24
R-Value Work:
0.18
R-Value Observed:
0.19
Space Group:
P 21 21 21
5YSY validation report
Macromolecular Entities
Structures with similar UniProt ID
Protein Blast
Polymer Type:polypeptide(L)
Molecule:Vitamin D3 receptor
Gene (Uniprot):VDR
Chain IDs:A
Chain Length:255
Number of Molecules:1
Biological Source:Homo sapiens
UniProt ID:P11473 Pfam ID:PF00104
Ligand Molecules
90L
Primary Citation
Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor.
Org. Biomol. Chem. 16 2448 2455 (2018)
PMID: 29560490 DOI: 10.1039/C8OB00158H

Abstact

Both 2α- and 2β-hydroxypropyl substituted 14-epi-1α,25-dihydroxy-19-nortachysterols were synthesized to study the human vitamin D receptor (hVDR) binding affinity, binding configurations, and interactions with amino acid residues in the ligand binding domain of hVDR by X-ray co-crystallographic analysis. In conjunction with our previous results on 14-epi-19-nortachysterol, 2-methylidene-, 2α-methyl-, 2β-methyl, and 2α-hydroxypropoxy-14-epi-19-nortachysterol, we propose a variety of effects of substitution at the C2 position in the 14-epi-19-nortachysterol skeleton on biological activities.

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Primary Citation of related structures
5YSY