5YT2 | pdb_00005yt2

Crystal structure of the human vitamin D receptor ligand binding domain complexed with (1R,2S,3R)-5-[(E)-2-{(1R,3aS,7aR)-1-[(R)-6-hydroxy-6-methylheptan-2-yl]-7a-methyl-2,3,3a,6,7,7a-hexahydro-1H-inden-4-yl}vinyl]-2-(3-hydroxypropyl)cyclohex-4-ene-1,3-diol

• PDB DOI: https://doi.org/10.2210/pdb5YT2/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-11-16 Released: 2018-04-11 
• Deposition Author(s): Takimoto-Kamimura, M., Kakuda, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work: 
  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 
  0.193 (Depositor) 

Starting Model: experimental

Literature

Effects of 2-substitution on 14-epi-19-nortachysterol-mediated biological events: based on synthesis and X-ray co-crystallographic analysis with the human vitamin D receptor.

Sawada, D., Kakuda, S., Takeuchi, A., Kawagoe, F., Takimoto-Kamimura, M., Kittaka, A.

(2018) Org Biomol Chem 16: 2448-2455

• PubMed: 29560490 
• DOI: https://doi.org/10.1039/C8OB00158H
• Primary Citation Related Structures: 
  5YSY, 5YT2


• PubMed Abstract: 
  

  Both 2α- and 2β-hydroxypropyl substituted 14-epi-1α,25-dihydroxy-19-nortachysterols were synthesized to study the human vitamin D receptor (hVDR) binding affinity, binding configurations, and interactions with amino acid residues in the ligand binding domain of hVDR by X-ray co-crystallographic analysis. In conjunction with our previous results on 14-epi-19-nortachysterol, 2-methylidene-, 2α-methyl-, 2β-methyl, and 2α-hydroxypropoxy-14-epi-19-nortachysterol, we propose a variety of effects of substitution at the C2 position in the 14-epi-19-nortachysterol skeleton on biological activities.

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Organizational Affiliation: 
• Faculty of Pharmaceutical Sciences, Teikyo University, Kaga, Itabashi, Tokyo 173-8605, Japan. [e-mail].
Teijin Institute for Bio-medical Research, Teijin Pharma Ltd, Hino, Tokyo 191-8512, Japan.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

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

Macromolecule Content 

• Total Structure Weight: 29.41 kDa 
• Atom Count: 2,331 
• Modeled Residue Count: 255 
• Deposited Residue Count: 255 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	255	Homo sapiens	Mutation(s): 0  Gene Names: VDR, NR1I1
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens) Explore P11473  Go to UniProtKB:  P11473
PHAROS:  P11473 GTEx:  ENSG00000111424

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
90O (Subject of Investigation/LOI)	B [auth A]	(1R,2S,3R)-5-[(E)-2-[(1R,3aS,7aR)-7a-methyl-1-[(2R)-6-methyl-6-oxidanyl-heptan-2-yl]-1,2,3,3a,6,7-hexahydroinden-4-yl]ethenyl]-2-(3-oxidanylpropyl)cyclohex-4-ene-1,3-diol C29 H48 O4 FSKKMLBYNCANGG-IATMLIOWSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.233 (Depositor), 0.236 (DCC) 
• R-Value Work:  0.191 (Depositor), 0.192 (DCC) 
• R-Value Observed: 0.193 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.565	α = 90
b = 51.565	β = 90
c = 132.49	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-04-11 
Deposition Author(s): Takimoto-Kamimura, M., Kakuda, S.

Revision History  

• Version 1.0: 2018-04-11
  Type: Initial release
  
• Version 1.1: 2018-04-18
  Changes: Data collection, Database references
• Version 1.2: 2023-11-22
  Changes: Data collection, Database references, Refinement description