› 3wt6

X-ray diffraction
2Å resolution

A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: Active vitamin D analogues with 22R-alkyl group

Released:
DOI: 10.2210/pdb3wt6/pdb
PDB entry 3wt6 coloured by chain, front view.
PDB entry 3wt6 coloured by chain, side view.
PDB entry 3wt6 coloured by chain, top view.
Source organisms:
Primary publication:
A mixed population of antagonist and agonist binding conformers in a single crystal explains partial agonism against vitamin D receptor: active vitamin D analogues with 22R-alkyl group.
Anami Y, Itoh T, Egawa D, Yoshimoto N, Yamamoto K
J Med Chem 57 4351-67 (2014)
PMID: 24742174

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
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: 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

1 bound ligand:
Ligand YA1 1 x YA1
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: PHOTON FACTORY BEAMLINE BL-5A
Spacegroup: C2
Unit cell:
a: 127.05Å b: 44.77Å c: 45.11Å
α: 90° β: 94.2° γ: 90°
R-values:
R R work R free
0.2 0.199 0.224
Expression systems:
  • Escherichia coli
  • Not provided

Quick links

Citations

7 review citations

No effects without causes: the Iron Dysregulation and Dormant Microbes hypothesis for chronic, inflammatory diseases.
Kell et al. (2018)
6 more

2 mentions without citation

Novel insights into the biotin carboxylase domain reactions of pyruvate carboxylase from Rhizobium etli.
Zeczycki et al. (2011)
1 more