› 7c7v

X-ray diffraction
2Å resolution

Vitamin D3 receptor/lithochoric acid derivative complex

Released:
DOI: 10.2210/pdb7c7v/pdb
Model geometry
Fit model/data
PDB entry 7c7v coloured by chain, front view.
PDB entry 7c7v coloured by chain, side view.
PDB entry 7c7v coloured by chain, top view.
Source organisms:
Primary publication:
Lithocholic Acid Derivatives as Potent Vitamin D Receptor Agonists.
Sasaki H, Masuno H, Kawasaki H, Yoshihara A, Numoto N, Ito N, Ishida H, Yamamoto K, Hirata N, Kanda Y, Kawachi E, Kagechika H, Tanatani A
J Med Chem 64 516-526 (2021)
PMID: 33369416

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-146463 (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 BL21(DE3)
UniProt:
  • Canonical: P13053 (Residues: 116-423; Coverage: 62%)
Gene names: Nr1i1, Vdr
Sequence domains: Ligand-binding domain of nuclear hormone receptor
Mediator of RNA polymerase II transcription subunit 1 Chain: C
Molecule details ›
Chain: C
Length: 13 amino acids
Theoretical weight: 1.57 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q15648 (Residues: 640-652; Coverage: 1%)
Gene names: ARC205, CRSP1, CRSP200, DRIP205, DRIP230, MED1, PBP, PPARBP, PPARGBP, RB18A, TRAP220, TRIP2

Ligands and Environments

2 bound ligands:
Ligand FKC 1 x FKC
Ligand FMT 1 x FMT
No modified residues

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: PHOTON FACTORY BEAMLINE BL-17A
Spacegroup: C2
Unit cell:
a: 158.045Å b: 36.898Å c: 39.486Å
α: 90° β: 96.963° γ: 90°
R-values:
R R work R free
0.201 0.198 0.268
Expression systems:
  • Escherichia coli BL21(DE3)
  • Not provided

Quick links

Citations

5 review citations

New Insights into Bile Acids Related Signaling Pathways in the Onset of Colorectal Cancer.
Caliceti et al. (2022)
4 more

1 mention without citation

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