1PQC

HUMAN LXR BETA HORMONE RECEPTOR COMPLEXED WITH T0901317


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 

wwPDB Validation   3D Report Full Report


This is version 1.3 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: https://doi.org/10.1074/jbc.M304842200
  • Primary Citation of Related Structures:  
    1PQ6, 1PQ9, 1PQC

  • 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 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Oxysterols receptor LXR-beta
A, B, C, D
253Homo sapiensMutation(s): 0 
Gene Names: NR1H2 OR LXRB OR UNR OR NER
UniProt & NIH Common Fund Data Resources
Find proteins for P55055 (Homo sapiens)
Explore P55055 
Go to UniProtKB:  P55055
PHAROS:  P55055
GTEx:  ENSG00000131408 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP55055
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Binding Affinity Annotations 
IDSourceBinding Affinity
444 BindingDB:  1PQC Ki: min: 17, max: 41 (nM) from 2 assay(s)
Kd: 103 (nM) from 1 assay(s)
IC50: min: 9, max: 2.60e+4 (nM) from 9 assay(s)
EC50: min: 4.7, max: 800 (nM) from 32 assay(s)
PDBBind:  1PQC IC50: 100 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.80 Å
  • R-Value Free: 0.262 
  • R-Value Work: 0.195 
  • R-Value Observed: 0.199 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 58.722α = 90
b = 103.262β = 90
c = 176.002γ = 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: Version format compliance
  • Version 1.3: 2024-02-14
    Changes: Data collection, Database references, Derived calculations