› 3aun

X-ray diffraction
1.81Å resolution

Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of DRIP 205

Released:
DOI: 10.2210/pdb3aun/pdb
PDB entry 3aun coloured by chain, front view.
PDB entry 3aun coloured by chain, side view.
PDB entry 3aun coloured by chain, top view.
Source organisms:
Primary publication:
Design, synthesis and X-ray crystallographic study of new nonsecosteroidal vitamin D receptor ligands.
Demizu Y, Takahashi T, Kaneko F, Sato Y, Okuda H, Ochiai E, Horie K, Takagi K, Kakuda S, Takimoto-Kamimura M, Kurihara M
Bioorg Med Chem Lett 21 6104-7 (2011)
PMID: 21889334

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: 265 amino acids
Theoretical weight: 30.06 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: B
Molecule details ›
Chain: B
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: synthetic construct
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 YR4 1 x YR4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P21212
Unit cell:
a: 44.237Å b: 136.521Å c: 47.334Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.198 0.196 0.237
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

3 review citations

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

1 mention without citation

A multidisciplinary approach disclosing unexplored Aflatoxin B1 roles in severe impairment of vitamin D mechanisms of action.
Persico et al. (2023)