› 2zxm

X-ray diffraction
3.01Å resolution

A New Class of Vitamin D Receptor Ligands that Induce Structural Rearrangement of the Ligand-binding Pocket

Released:
DOI: 10.2210/pdb2zxm/pdb
PDB entry 2zxm coloured by chain, front view.
PDB entry 2zxm coloured by chain, side view.
PDB entry 2zxm coloured by chain, top view.
Source organisms:
Primary publication:
A new class of vitamin D analogues that induce structural rearrangement of the ligand-binding pocket of the receptor.
Inaba Y, Yoshimoto N, Sakamaki Y, Nakabayashi M, Ikura T, Tamamura H, Ito N, Shimizu M, Yamamoto K
J Med Chem 52 1438-49 (2009)
PMID: 19193059

Function and Biology Details

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

Structure analysis Details

Assemblies composition:
monomeric
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-106654 (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
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: Xenopus tropicalis
Expression system: Not provided
UniProt:
  • Canonical: A1L0Z0 (Residues: 624-636; Coverage: 1%)
Gene name: med1

Ligands and Environments

1 bound ligand:
Ligand JB1 1 x JB1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-6A
Spacegroup: C2
Unit cell:
a: 153.252Å b: 43.424Å c: 42.369Å
α: 90° β: 95.97° γ: 90°
R-values:
R R work R free
0.226 0.226 0.295
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

Vitamin D receptor ligands: the impact of crystal structures.
Carlberg et al. (2012)
6 more

3 mentions without citation

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