› 3a40

X-ray diffraction
1.45Å resolution

Crystal structure of the human VDR ligand binding domain bound to the synthetic agonist compound 2alpha-methyl-AMCR277B(C23R)

Released:
DOI: 10.2210/pdb3a40/pdb
PDB entry 3a40 coloured by chain, front view.
PDB entry 3a40 coloured by chain, side view.
PDB entry 3a40 coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Structure-function relationships and crystal structures of the vitamin D receptor bound 2 alpha-methyl-(20S,23S)- and 2 alpha-methyl-(20S,23R)-epoxymethano-1 alpha,25-dihydroxyvitamin D3.
Antony P, Sigüeiro R, Huet T, Sato Y, Ramalanjaona N, Rodrigues LC, Mouriño A, Moras D, Rochel N
J Med Chem 53 1159-71 (2010)
PMID: 20070104

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-145848 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vitamin D3 receptor Chain: X
Molecule details ›
Chain: X
Length: 263 amino acids
Theoretical weight: 29.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P11473 (Residues: 118-427; Coverage: 61%)
Gene names: NR1I1, VDR
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Structure domains: Retinoid X Receptor

Ligands and Environments

2 bound ligands:
Ligand 23R 1 x 23R
Ligand SO4 2 x SO4
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID29
Spacegroup: P212121
Unit cell:
a: 44.969Å b: 51.496Å c: 131.91Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.162 0.16 0.196
Expression system: Escherichia coli

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Citations

8 review citations

Anticancer steroids: linking natural and semi-synthetic compounds.
Salvador et al. (2013)
7 more

3 mentions without citation

Exposure to p,p'-DDE or dieldrin during the reproductive season alters hepatic CYP expression in largemouth bass (Micropterus salmoides).
Barber et al. (2007)
2 more