PDBe 5xpl

X-ray diffraction
2.05Å resolution

Crystal structure of VDR-LBD complexed with 22S-butyl-25-hydroxyphenyl-2-methylidene-19,26,27-trinor-25-oxo-1-hydroxyvitamin D3

Released:

Function and Biology Details

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Vitamin D3 receptor Chain: A
Molecule details ›
Chain: A
Length: 271 amino acids
Theoretical weight: 30.6 KDa
Source organism: Rattus norvegicus
Expression system: Escherichia coli
UniProt:
  • Canonical: P13053 (Residues: 116-423; Coverage: 62%)
Gene names: Nr1i1, Vdr
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Nuclear receptor coactivator 2 Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.59 KDa
Source organism: Homo sapiens
Expression system: synthetic construct
UniProt:
  • Canonical: Q15596 (Residues: 740-752; Coverage: 1%)
Gene names: BHLHE75, NCOA2, SRC2, TIF2

Ligands and Environments

1 bound ligand:

No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: C2
Unit cell:
a: 128.78Å b: 44.91Å c: 45.52Å
α: 90° β: 93.62° γ: 90°
R-values:
R R work R free
0.189 0.186 0.242
Expression systems:
  • Escherichia coli
  • synthetic construct