› 1rjk

X-ray diffraction
1.99Å resolution

crystal structure of the rat vitamin D receptor ligand binding domain complexed with 2MD and a synthetic peptide containing the NR2 box of DRIP 205

Released:
DOI: 10.2210/pdb1rjk/pdb
PDB entry 1rjk coloured by chain, front view.
PDB entry 1rjk coloured by chain, side view.
PDB entry 1rjk coloured by chain, top view.
Source organisms:
Primary publication:
Molecular structure of the rat vitamin D receptor ligand binding domain complexed with 2-carbon-substituted vitamin D3 hormone analogues and a LXXLL-containing coactivator peptide.
Vanhooke JL, Benning MM, Bauer CB, Pike JW, DeLuca HF
Biochemistry 43 4101-10 (2004)
PMID: 15065852

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
hetero tetramer
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: 292 amino acids
Theoretical weight: 32.98 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: Not provided
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 VDZ 1 x VDZ
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ENRAF-NONIUS FR591
Spacegroup: C2
Unit cell:
a: 154.6Å b: 43.292Å c: 41.848Å
α: 90° β: 96.07° γ: 90°
R-values:
R R work R free
0.188 0.185 0.244
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

20 review citations

Vitamin D: Metabolism, Molecular Mechanism of Action, and Pleiotropic Effects.
Christakos et al. (2016)
19 more

7 mentions without citation

CABS-dock web server for the flexible docking of peptides to proteins without prior knowledge of the binding site.
Kurcinski et al. (2015)
6 more