1X7J

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH GENISTEIN

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 

wwPDB Validation   3D Report Full Report


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


Literature

Understanding the Selectivity of Genistein for Human Estrogen Receptor-Beta Using X-Ray Crystallography and Computational Methods

Manas, E.S., Xu, Z.B., Unwalla, R.J., Somers, W.S.

(2004) Structure 12: 2197-2207

  • DOI: 10.1016/j.str.2004.09.015
  • Primary Citation of Related Structures:  
    1X7J, 1X7R

  • PubMed Abstract: 

    • We present X-ray crystallographic and molecular modeling studies of estrogen receptors-alpha and -beta complexed with the estrogen receptor-beta-selective phytoestrogen genistein, and coactivator-derived NR box peptides containing an LXXLL motif. We demonstrate that the ligand binding mode is essentially identical when genistein is bound to both isoforms, despite the considerably weaker affinity of this ligand for estrogen receptor-alpha ...

    We present X-ray crystallographic and molecular modeling studies of estrogen receptors-alpha and -beta complexed with the estrogen receptor-beta-selective phytoestrogen genistein, and coactivator-derived NR box peptides containing an LXXLL motif. We demonstrate that the ligand binding mode is essentially identical when genistein is bound to both isoforms, despite the considerably weaker affinity of this ligand for estrogen receptor-alpha. In addition, we examine subtle differences between binding site residues, providing an explanation for why genistein is modestly selective for the beta isoform. To this end, we also present the results of quantum chemical studies and thermodynamic arguments that yield insight to the nature of the interactions leading to estrogen receptor-beta selectivity. The importance of our analysis to structure-based drug design is discussed.

    Organizational Affiliation: 

    Department of Chemical and Screening Sciences, Wyeth Research, 500 Arcola Road, Collegeville, PA 19426, USA. manase@wyeth.com



Macromolecules
Find similar proteins by: 
(by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Estrogen receptor betaA, B240Homo sapiensMutation(s): 0 
Gene Names: ESR2, NR3A2, ESTRB
Find proteins for Q92731 (Homo sapiens)
Explore Q92731 
Go to UniProtKB:  Q92731
NIH Common Fund Data Resources
PHAROS:  Q92731
GTEx:  ENSG00000140009
Protein Feature View
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  • Reference Sequence
  • Find similar proteins by:  Sequence   |   Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
STEROID RECEPTOR COACTIVATOR-1C, D13N/AMutation(s): 0 
Protein Feature View
Expand
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GEN
Query on GEN
Download Ideal Coordinates CCD File 
 E [auth A], F [auth B]GENISTEIN
C15 H10 O5
TZBJGXHYKVUXJN-UHFFFAOYSA-N		 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
GENEC50:  2.4000000953674316   nM  BindingDB
GENIC50:  9   nM  Binding MOAD
GENIC50:  83   nM  BindingDB
GENEC50:  73   nM  BindingDB
GENIC50:  61   nM  BindingDB
GENIC50:  990   nM  BindingDB
GENIC50:  4   nM  BindingDB
GENKi:  24   nM  BindingDB
GENEC50:  4.099999904632568   nM  BindingDB
GENIC50:  18   nM  BindingDB
GENEC50:  6   nM  BindingDB
GENIC50:  98.69999694824219   nM  BindingDB
GENIC50:  6.800000190734863   nM  BindingDB
GENEC50:  28   nM  BindingDB
GENIC50:  200   nM  BindingDB
GENIC50:  9.699999809265137   nM  BindingDB
GENIC50:  10   nM  BindingDB
GENIC50:  1.2999999523162842   nM  BindingDB
GENEC50:  200   nM  BindingDB
GENIC50:  25   nM  BindingDB
GENIC50:  390   nM  BindingDB
GENIC50:  395   nM  BindingDB
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.282 
  • R-Value Work: 0.232 
  • R-Value Observed: 0.236 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.231α = 90
b = 87.667β = 90
c = 100.113γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2005-03-01
    Type: Initial release
  • Version 1.1: 2008-04-30
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance