› 5ysy

X-ray diffraction
2Å resolution

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

Released:
DOI: 10.2210/pdb5ysy/pdb
PDB entry 5ysy coloured by chain, front view.
PDB entry 5ysy coloured by chain, side view.
PDB entry 5ysy coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
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.
Sawada D, Kakuda S, Takeuchi A, Kawagoe F, Takimoto-Kamimura M, Kittaka A
Org Biomol Chem 16 2448-2455 (2018)
PMID: 29560490

Function and Biology Details

Biochemical function:
Biological process:
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145848 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vitamin D3 receptor Chain: A
Molecule details ›
Chain: A
Length: 255 amino acids
Theoretical weight: 28.95 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11473 (Residues: 118-423; Coverage: 60%)
Gene names: NR1I1, VDR
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor

Ligands and Environments

1 bound ligand:
Ligand 90L 1 x 90L
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE AR-NE3A
Spacegroup: P212121
Unit cell:
a: 44.682Å b: 51.538Å c: 132.651Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.189 0.242
Expression system: Escherichia coli

Quick links

Citations

2 review citations

Vitamin D and Its Synthetic Analogs.
Maestro et al. (2019)
1 more

2 mentions without citation

Beyond Antioxidant Effects: Nature-Based Templates Unveil New Strategies for Neurodegenerative Diseases.
Bacci et al. (2021)
1 more