3X31

Crystal structure of the human vitamin D receptor ligand binding domain complexed with 7,8-cis-14-epi-1a,25-Dihydroxy-19-norvitamin D3

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 1.2 of the entry. See complete history. 


Literature

Revisiting the 7,8-cis-vitamin D3 derivatives: synthesis, evaluating the biological activity, and study of the binding configuration

Sawada, D., Saito, H., Kakuda, S., Takimoto-Kamimura, M., Matsumoto, Y., Takagi, K., Ochiai, E., Kittaka, A.

To be published.

Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Vitamin D3 receptor263Homo sapiensMutation(s): 0 
Gene Names: NR1I1, VDR
UniProt & NIH Common Fund Data Resources
Find proteins for P11473 (Homo sapiens)
Explore P11473 
Go to UniProtKB:  P11473
PHAROS:  P11473
GTEx:  ENSG00000111424 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP11473
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
41V
Query on 41V
Download Ideal Coordinates CCD File 
B [auth A](1R,3R,7Z,14beta,17alpha)-17-[(2R)-6-hydroxy-6-methylheptan-2-yl]-9,10-secoestra-5,7-diene-1,3-diol
C26 H44 O3
PKFBWEUIKKCWEW-VWYYVUTKSA-N
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.11 Å
  • R-Value Free: 0.299 
  • R-Value Work: 0.237 
  • R-Value Observed: 0.240 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 44.369α = 90
b = 51.508β = 90
c = 131.52γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
MOLREPphasing
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Ligand Structure Quality Assessment 


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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2016-01-13
    Type: Initial release
  • Version 1.1: 2017-08-23
    Changes: Refinement description, Source and taxonomy
  • Version 1.2: 2024-03-20
    Changes: Data collection, Database references, Derived calculations