› 2ham

X-ray diffraction
1.9Å resolution

Crystal structure of VDR LBD complexed to 2alpha-propyl-calcitriol

Released:
DOI: 10.2210/pdb2ham/pdb
PDB 2ham coloured by chain and viewed from the front.
PDB 2ham coloured by chain and viewed from the side.
PDB 2ham coloured by chain and viewed from the top.
Source organism: Homo sapiens
Primary publication:
Probing a water channel near the A-ring of receptor-bound 1 alpha,25-dihydroxyvitamin D3 with selected 2 alpha-substituted analogues.
Hourai S, Fujishima T, Kittaka A, Suhara Y, Takayama H, Rochel N, Moras D
J. Med. Chem. 49 5199-205 (2006)
PMID: 16913708

Function and Biology Details

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

Structure analysis Details

Assembly composition:
monomeric (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Vitamin D3 receptor Chain: A
Molecule details ›
Chain: A
Length: 263 amino acids
Theoretical weight: 29.81 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
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

1 bound ligand:
Ligand C33 1 x C33
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ESRF BEAMLINE ID14-4
Spacegroup: P212121
Unit cell:
a: 45.06Å b: 51.326Å c: 131.304Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.186 0.186 0.216
Expression system: Escherichia coli BL21(DE3)

Quick links

Citations

13 review citations

The Synthesis and Biological Evaluation of D-Ring-Modified Vitamin D Analogues.
Kawagoe et al. (2021)
12 more