› 3wwr

X-ray diffraction
3.18Å resolution

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 1-((((1S,2R,6R,Z)-2,6-dihydroxy-4-((E)-2-((1R,3aS,7aR)-1-((R)-6-hydroxy-6-methylheptan-2-yl)-7a-methylhexahydro-1H-inden-4(2H)-ylidene)ethylidene)-3-methylenecyclohexyl)oxy)methyl)cyclopropanecarbonitrile

Released:
DOI: 10.2210/pdb3wwr/pdb
PDB entry 3wwr coloured by chain, front view.
PDB entry 3wwr coloured by chain, side view.
PDB entry 3wwr coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis and biological activities of vitamin D3 derivatives with cyanoalkyl side chain at C-2 position.
Saitoh H, Watanabe H, Kakuda S, Takimoto-Kamimura M, Takagi K, Takeuchi A, Takenouchi K
J Steroid Biochem Mol Biol 148 27-30 (2015)
PMID: 25500068

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: 263 amino acids
Theoretical weight: 29.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11473 (Residues: 118-427; Coverage: 61%)
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 3AJ 1 x 3AJ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P212121
Unit cell:
a: 45.167Å b: 51.826Å c: 132.384Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.249 0.247 0.291
Expression system: Escherichia coli

Quick links

Citations

2 review citations

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