› 2o4j

X-ray diffraction
1.74Å resolution

Crystal Structure of Rat Vitamin D Receptor Ligand Binding Domain Complexed with VitIII 17-20Z and the NR2 Box of DRIP 205

Released:
DOI: 10.2210/pdb2o4j/pdb
PDB entry 2o4j coloured by chain, front view.
PDB entry 2o4j coloured by chain, side view.
PDB entry 2o4j coloured by chain, top view.
Source organisms:
Primary publication:
New analogs of 2-methylene-19-nor-(20S)-1,25-dihydroxyvitamin D3 with conformationally restricted side chains: evaluation of biological activity and structural determination of VDR-bound conformations.
Vanhooke JL, Tadi BP, Benning MM, Plum LA, DeLuca HF
Arch Biochem Biophys 460 161-5 (2007)
PMID: 17227670

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 VD4 1 x VD4
No modified residues

Experiments and Validation Details

Entry percentile scores
Spacegroup: C2
Unit cell:
a: 155.5Å b: 42.4Å c: 41.9Å
α: 90° β: 96.5° γ: 90°
R-values:
R R work R free
0.201 0.199 0.246
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

5 review citations

Vitamin D, disease and therapeutic opportunities.
Plum et al. (2010)
4 more

3 mentions without citation

Benchmarking of different molecular docking methods for protein-peptide docking.
Agrawal et al. (2019)
2 more