3W0A

Crystal Structure Analysis of Vitamin D receptor

• PDB DOI: https://doi.org/10.2210/pdb3W0A/pdb

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


• Deposited: 2012-10-25 Released: 2013-11-13 
• Deposition Author(s): Itoh, S., Iijima, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 

Literature

structure analysis of vitamin D3 receptor

Kashiwagi, H., Ohta, M., Ono, Y., Itoh, S., Iijima, S., Sato, H., Takahashi, T.

To be published.

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: 29.32 kDa 
• Atom Count: 2,295 
• Modelled Residue Count: 250 
• Deposited Residue Count: 253 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Vitamin D3 receptor	A	253	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
DS5	B [auth A]	(4S)-4-hydroxy-5-[2-methyl-4-(3-{3-methyl-4-[4,4,4-trifluoro-3-hydroxy-3-(trifluoromethyl)but-1-yn-1-yl]phenyl}pentan-3-yl)phenoxy]pentanoic acid C29 H32 F6 O5 BMRRFNRRIWOMAT-QHCPKHFHSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 0.236 
• R-Value Work: 0.192 
• R-Value Observed: 0.194 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 44.619	α = 90
b = 51.803	β = 90
c = 132.513	γ = 90

Software Package:

Software Name	Purpose
MOSFLM	data reduction
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-11-13 
Deposition Author(s): Itoh, S., Iijima, S.

Revision History  

• Version 1.0: 2013-11-13
  Type: Initial release
  
• Version 1.1: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations