› 3vt6

X-ray diffraction
2.3Å resolution

Crystal structure of rat VDR-LBD with 2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3

Released:
DOI: 10.2210/pdb3vt6/pdb
PDB entry 3vt6 coloured by chain, front view.
PDB entry 3vt6 coloured by chain, side view.
PDB entry 3vt6 coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
Crystal structures of hereditary vitamin D-resistant rickets-associated vitamin D receptor mutants R270L and W282R bound to 1,25-dihydroxyvitamin D3 and synthetic ligands.
Nakabayashi M, Tsukahara Y, Iwasaki-Miyamoto Y, Mihori-Shimazaki M, Yamada S, Inaba S, Oda M, Shimizu M, Makishima M, Tokiwa H, Ikura T, Ito N
J Med Chem 56 6745-60 (2013)
PMID: 23944708

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
hetero dimer (preferred)
monomeric
Assembly name:
PDBe Complex ID:
PDB-CPX-146456 (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
COACTIVATOR PEPTIDE DRIP Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Rattus norvegicus
Expression system: Not provided

Ligands and Environments

1 bound ligand:
Ligand 5YI 1 x 5YI
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: C2
Unit cell:
a: 153.734Å b: 42.724Å c: 42.271Å
α: 90° β: 95.55° γ: 90°
R-values:
R R work R free
0.21 0.21 0.245
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

6 review citations

Vitamin D and Its Synthetic Analogs.
Maestro et al. (2019)
5 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)