3AUN | pdb_00003aun

Crystal structure of the rat vitamin D receptor ligand binding domain complexed with YR335 and a synthetic peptide containing the NR2 box of DRIP 205

• PDB DOI: https://doi.org/10.2210/pdb3AUN/pdb

• Classification: TRANSCRIPTION
• Organism(s): Rattus norvegicus, synthetic construct
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-02-10 Released: 2012-02-15 
• Deposition Author(s): Kakuda, S., Takimoto-Kamimura, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free: 
  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work: 
  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 
  0.198 (Depositor) 

Starting Model: experimental

Literature

Design, synthesis and X-ray crystallographic study of new nonsecosteroidal vitamin D receptor ligands

Demizu, Y., Takahashi, T., Kaneko, F., Sato, Y., Okuda, H., Ochiai, E., Horie, K., Takagi, K., Kakuda, S., Takimoto-Kamimura, M., Kurihara, M.

(2011) Bioorg Med Chem Lett 21: 6104-6107

• PubMed: 21889334 
• DOI: https://doi.org/10.1016/j.bmcl.2011.08.047
• Primary Citation of Related Structures:  
  3AUN


• PubMed Abstract: 
  

  We designed and synthesized nonsecosteroidal vitamin D receptor (VDR) ligands that formed H-bonds with six amino acid residues (Tyr143, Ser233, Arg270, Ser274, His301 and His393) of the VDR ligand-binding domain. The ligand YR335 exhibited potent transcriptional activity, which was comparable to those of 1α,25-dihydroxyvitamin D(3) and YR301. The crystal structure of the complex formed between YR335 and the VDR ligand-binding domain was solved, which revealed that YR335 formed H-bonds with the six amino acid residues mentioned above.

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Organizational Affiliation: 

Division of Organic Chemistry, National Institute of Health Sciences, 1-18-1, Kamiyoga, Setagaya, Tokyo 158-8501, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 32.1 kDa 
• Atom Count: 2,181 
• Modelled Residue Count: 247 
• Deposited Residue Count: 278 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	265	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P13053 (Rattus norvegicus) Explore P13053  Go to UniProtKB:  P13053

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
DRIP 205 NR2 box peptide	B	13	synthetic construct	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for Q15648 (Homo sapiens) Explore Q15648  Go to UniProtKB:  Q15648
PHAROS:  Q15648 GTEx:  ENSG00000125686

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
YR4	C [auth A]	(2R)-2-{4-[3-(4-{[(2R)-2-hydroxy-3,3-dimethylbutyl]oxy}-3-methylphenyl)pentan-3-yl]-2-methylphenoxy}butane-1,4-diol C29 H44 O5 DKNLNQKPISQAEP-SQHAQQRYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.81 Å
• R-Value Free:  0.237 (Depositor), 0.240 (DCC) 
• R-Value Work:  0.196 (Depositor), 0.190 (DCC) 
• R-Value Observed: 0.198 (Depositor) 

Space Group: P 2₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.237	α = 90
b = 136.521	β = 90
c = 47.334	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
MOLREP	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-15 
Deposition Author(s): Kakuda, S., Takimoto-Kamimura, M.

Revision History  

• Version 1.0: 2012-02-15
  Type: Initial release
  
• Version 1.1: 2012-08-01
  Changes: Database references
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2017-08-23
  Changes: Source and taxonomy
• Version 1.4: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description