3A78

Crystal structure of the human VDR ligand binding domain bound to the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of the activation of the human Vitamin D receptor by the natural metabolite 1alpha,25-dihydroxy-3-epi-vitamin D3

Molnar, F.Sigueiro, R.Sato, Y.Antony, P.Mourino, A.Rochel, N.Moras, D.

To be published.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Vitamin D3 receptor
A
263Homo sapiensMutation(s): 0 
Gene Names: VDR (NR1I1)
Find proteins for P11473 (Homo sapiens)
Go to Gene View: VDR
Go to UniProtKB:  P11473
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
SO4
Query on SO4

Download SDF File 
Download CCD File 
A
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
3EV
Query on 3EV

Download SDF File 
Download CCD File 
A
(1S,3S,5Z,7E,14beta,17alpha)-9,10-secocholesta-5,7,10-triene-1,3,25-triol
1alpha,25-dihydroxy-3-epi-vitamin D3
C27 H44 O3
GMRQFYUYWCNGIN-GNVXBELXSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.203 
  • R-Value Work: 0.172 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 44.889α = 90.00
b = 51.120β = 90.00
c = 132.196γ = 90.00
Software Package:
Software NamePurpose
REFMACphasing
SCALAdata scaling
MOSFLMdata reduction
REFMACrefinement
MxCuBEdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2010-10-13
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2017-08-16
    Type: Advisory, Refinement description, Source and taxonomy