› 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 1rjk coloured by chain and viewed from the front.
PDB 1rjk coloured by chain and viewed from the side.
PDB 1rjk coloured by chain and viewed from the top.
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
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

17 review citations

Alternative binding sites at the vitamin D receptor and their ligands.
Mutchie et al. (2019)
16 more

2 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)
1 more