1PQ6

HUMAN LXR BETA HORMONE RECEPTOR / GW3965 COMPLEX


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 

wwPDB Validation   3D Report Full Report


This is version 1.2 of the entry. See complete history


Literature

The three-dimensional structure of the liver X receptor beta reveals a flexible ligand-binding pocket that can accommodate fundamentally different ligands.

Farnegardh, M.Bonn, T.Sun, S.Ljunggren, J.Ahola, H.Wilhelmsson, A.Gustafsson, J.-A.Carlquist, M.

(2003) J Biol Chem 278: 38821-38828

  • DOI: 10.1074/jbc.M304842200
  • Primary Citation of Related Structures:  
    1PQC, 1PQ9, 1PQ6

  • PubMed Abstract: 
  • The structures of the liver X receptor LXRbeta (NR1H2) have been determined in complexes with two synthetic ligands, T0901317 and GW3965, to 2.1 and 2.4 A, respectively. Together with its isoform LXRalpha (NR1H3) it regulates target genes involved in metabolism and transport of cholesterol and fatty acids ...

    The structures of the liver X receptor LXRbeta (NR1H2) have been determined in complexes with two synthetic ligands, T0901317 and GW3965, to 2.1 and 2.4 A, respectively. Together with its isoform LXRalpha (NR1H3) it regulates target genes involved in metabolism and transport of cholesterol and fatty acids. The two LXRbeta structures reveal a flexible ligand-binding pocket that can adjust to accommodate fundamentally different ligands. The ligand-binding pocket is hydrophobic but with polar or charged residues at the two ends of the cavity. T0901317 takes advantage of this by binding to His-435 close to H12 while GW3965 orients itself with its charged group in the opposite direction. Both ligands induce a fixed "agonist conformation" of helix H12 (also called the AF-2 domain), resulting in a transcriptionally active receptor.


    Organizational Affiliation

    Karo Bio AB, NOVUM, Karolinska Institute, Huddinge University Hosptial, Sweden. mathias.farnegardh@karobio.se



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Oxysterols receptor LXR-beta ABCD253Homo sapiensMutation(s): 0 
Gene Names: NR1H2 OR LXRB OR UNR OR NERNR1H2LXRBNERUNR
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
NIH Common Fund Data Resources
PHAROS:  P55055
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
965
Query on 965

Download Ideal Coordinates CCD File 
A, B, D
[3-(3-{[2-chloro-3-(trifluoromethyl)benzyl](2,2-diphenylethyl)amino}propoxy)phenyl]acetic acid
C33 H31 Cl F3 N O3
NAXSRXHZFIBFMI-UHFFFAOYSA-N
 Ligand Interaction
IPA
Query on IPA

Download Ideal Coordinates CCD File 
A, B
ISOPROPYL ALCOHOL
C3 H8 O
KFZMGEQAYNKOFK-UHFFFAOYSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
965IC50:  30   nM  BindingDB
965EC50:  27   nM  BindingDB
965EC50:  25   nM  BindingDB
965EC50:  400   nM  BindingDB
965EC50:  410   nM  BindingDB
965EC50:  420   nM  BindingDB
965EC50:  501   nM  BindingDB
965EC50:  130   nM  BindingDB
965IC50 :  7.940000057220459   nM  PDBBind
965EC50:  78   nM  BindingDB
965EC50:  310   nM  BindingDB
965EC50:  5   nM  BindingDB
965EC50:  20   nM  BindingDB
965IC50:  40   nM  BindingDB
965EC50:  390   nM  BindingDB
965IC50:  12   nM  BindingDB
965IC50:  7.900000095367432   nM  BindingDB
965IC50:  23   nM  BindingDB
965EC50:  40   nM  BindingDB
965EC50:  35   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.40 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.207 
  • R-Value Observed: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.717α = 90
b = 98.929β = 90
c = 175.815γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
MOSFLMdata reduction
CCP4data scaling
AMoREphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-09-09
    Type: Initial release
  • Version 1.1: 2008-04-29
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance