1IE8

Crystal Structure Of The Nuclear Receptor For Vitamin D Ligand Binding Domain Bound to KH1060


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.212 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal structures of the vitamin D receptor complexed to superagonist 20-epi ligands.

Tocchini-Valentini, G.Rochel, N.Wurtz, J.M.Mitschler, A.Moras, D.

(2001) Proc.Natl.Acad.Sci.USA 98: 5491-5496

  • DOI: 10.1073/pnas.091018698
  • Primary Citation of Related Structures:  1IE9

  • PubMed Abstract: 
  • The crystal structures of the ligand-binding domain (LBD) of the vitamin D receptor complexed to 1alpha,25(OH)(2)D(3) and the 20-epi analogs, MC1288 and KH1060, show that the protein conformation is identical, conferring a general character to the ob ...

    The crystal structures of the ligand-binding domain (LBD) of the vitamin D receptor complexed to 1alpha,25(OH)(2)D(3) and the 20-epi analogs, MC1288 and KH1060, show that the protein conformation is identical, conferring a general character to the observation first made for retinoic acid receptor (RAR) that, for a given LBD, the agonist conformation is unique, the ligands adapting to the binding pocket. In all complexes, the A- to D-ring moieties of the ligands adopt the same conformation and form identical contacts with the protein. Differences are observed only for the 17beta-aliphatic chains that adapt their conformation to anchor the 25-hydroxyl group to His-305 and His-397. The inverted geometry of the C20 methyl group induces different paths of the aliphatic chains. The ligands exhibit a low-energy conformation for MC1288 and a more strained conformation for the two others. KH1060 compensates this energy cost by additional contacts. Based on the present data, the explanation of the superagonist effect is to be found in higher stability and longer half-life of the active complex, thereby excluding different conformations of the ligand binding domain.


    Organizational Affiliation

    Laboratoire de Biologie et Génomique Structurales, Institut de Génétique et de Biologie Moléculaire et Cellulaire, Centre National de la Recherche Scientifique/Institut National de la Santé et de la Recherche Médicale/Université Louis Pasteur, France.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
VITAMIN D3 RECEPTOR
A
259Homo sapiensGene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens)
Go to Gene View: VDR
Go to UniProtKB:  P11473
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
KH1
Query on KH1

Download SDF File 
Download CCD File 
A
5-(2-{1-[1-(4-ETHYL-4-HYDROXY-HEXYLOXY)-ETHYL]-7A-METHYL-OCTAHYDRO-INDEN-4-YLIDENE}-ETHYLIDENE)-4-METHYLENE-CYCLOHEXANE-1,3-DIOL
1ALPHA,25-DIHYDROXYL-20-EPI-22-OXA-24,26,27-TRIHOMO VITAMIN D3
C29 H48 O4
KLZOTDOJMRMLDX-YBBVPDDNSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.52 Å
  • R-Value Free: 0.230 
  • R-Value Work: 0.212 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.490α = 90.00
b = 51.870β = 90.00
c = 131.390γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
CCP4data scaling
DENZOdata reduction
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-05-16
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance
  • Version 1.3: 2017-08-16
    Type: Refinement description, Source and taxonomy