› 3vhw

X-ray diffraction
2.43Å resolution

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 4-MP

Released:
DOI: 10.2210/pdb3vhw/pdb
PDB entry 3vhw coloured by chain, front view.
PDB entry 3vhw coloured by chain, side view.
PDB entry 3vhw coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Synthesis of novel C-2 substituted vitamin D derivatives having ringed side chains and their biological evaluation on bone.
Saito H, Takagi K, Horie K, Kakuda S, Takimoto-Kamimura M, Ochiai E, Chida T, Harada Y, Takenouchi K, Kittaka A
J Steroid Biochem Mol Biol 136 3-8 (2013)
PMID: 23416104

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: A
Molecule details ›
Chain: A
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

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

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL32B2
Spacegroup: P212121
Unit cell:
a: 44.975Å b: 51.47Å c: 131.264Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.192 0.189 0.247
Expression system: Escherichia coli

Quick links

Citations

1 review citation

Structural considerations of vitamin D signaling.
Molnár F. (2014)

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)