› 2zlc

X-ray diffraction
2Å resolution

2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation and crystal structure

Released:
DOI: 10.2210/pdb2zlc/pdb
PDB entry 2zlc coloured by chain, front view.
PDB entry 2zlc coloured by chain, side view.
PDB entry 2zlc coloured by chain, top view.
Source organism: Rattus norvegicus
Primary publication:
2-Substituted-16-ene-22-thia-1alpha,25-dihydroxy-26,27-dimethyl-19-norvitamin D3 analogs: Synthesis, biological evaluation, and crystal structure.
Shimizu M, Miyamoto Y, Takaku H, Matsuo M, Nakabayashi M, Masuno H, Udagawa N, DeLuca HF, Ikura T, Ito N
Bioorg Med Chem 16 6949-64 (2008)
PMID: 18539034

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146452 (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 VDX 1 x VDX
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: C2
Unit cell:
a: 153.859Å b: 41.998Å c: 41.951Å
α: 90° β: 96.06° γ: 90°
R-values:
R R work R free
0.225 0.225 0.261
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

9 review citations

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

4 mentions without citation

Lithocholic Acid Amides as Potent Vitamin D Receptor Agonists.
Yoshihara et al. (2022)
3 more