› 5xpm

X-ray diffraction
2.2Å resolution

Crystal structure of VDR-LBD complexed with 22S-Butyl-25RS-(hydroxyphenyl)-25-methoxy-2-methylidene-19,26,27-trinor-1-hydroxyvitamin D3

Released:
DOI: 10.2210/pdb5xpm/pdb
PDB entry 5xpm coloured by chain, front view.
PDB entry 5xpm coloured by chain, side view.
PDB entry 5xpm coloured by chain, top view.
Source organisms:
Primary publication:
Vitamin D Analogues with a p-Hydroxyphenyl Group at the C25 Position: Crystal Structure of Vitamin D Receptor Ligand-Binding Domain Complexed with the Ligand Explains the Mechanism Underlying Full Antagonistic Action.
Kato A, Yamao M, Hashihara Y, Ishida H, Itoh T, Yamamoto K
J Med Chem 60 8394-8406 (2017)
PMID: 28954197

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146463 (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
Structure domains: Retinoid X Receptor
Mediator of RNA polymerase II transcription subunit 1 Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Homo sapiens
Expression system: synthetic construct
UniProt:
  • Canonical: Q15648 (Residues: 640-652; Coverage: 1%)
Gene names: ARC205, CRSP1, CRSP200, DRIP205, DRIP230, MED1, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2

Ligands and Environments

1 bound ligand:
Ligand 8C0 1 x 8C0
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: C2
Unit cell:
a: 153Å b: 41.84Å c: 42.25Å
α: 90° β: 96.69° γ: 90°
R-values:
R R work R free
0.199 0.196 0.248
Expression systems:
  • Escherichia coli
  • synthetic construct

Quick links

Citations

3 review citations

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