Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 57531.95 
• Atom Count: 3754 
• Residue Count: 506 
• Unique protein chains: 2

1X7J

CRYSTAL STRUCTURE OF ESTROGEN RECEPTOR BETA COMPLEXED WITH GENISTEIN

• DOI: 10.2210/pdb1X7J/pdb

• Classification: TRANSCRIPTION
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)


• Deposited: 2004-08-14 Released: 2005-03-01 
• Deposition Author(s): Manas, E.S., Xu, Z.B., Unwalla, R.J., Somers, W.S.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.282 
• R-Value Work: 0.232 

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

• PubMed: 15576033 
• DOI: 10.1016/j.str.2004.09.015
• Primary Citation of Related Structures:  
  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. 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. [e-mail]

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Estrogen receptor beta	A, B	240	Homo sapiens	Mutation(s): 0  Gene Names: ESR2 (ESTRB, NR3A2)
Find proteins for Q92731 (Homo sapiens) Go to Gene View: ESR2 Go to UniProtKB:  Q92731

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
STEROID RECEPTOR COACTIVATOR-1	C, D	13	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
GEN	A, B	GENISTEIN 5,7-DIHYDROXY-3-(4-HYDROXYPHENYL)-4H-1-BENZOPYRAN-4-ONE; 4',5,7-TRIHYDROXYISOFLAVONE; PRUNETOL; GENISTEOL C15 H10 O5 TZBJGXHYKVUXJN-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
GEN	IC50: 9 nM BINDINGMOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.3 Å
• R-Value Free: 0.282 
• R-Value Work: 0.232 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length (Å)	Angle (°)
a = 52.231	α = 90.00
b = 87.667	β = 90.00
c = 100.113	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
HKL-2000	data reduction
AMoRE	phasing
HKL-2000	data collection
CNS	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2004-08-14 
• Released Date: 2005-03-01 
• Deposition Author(s): Manas, E.S., Xu, Z.B., Unwalla, R.J., Somers, W.S.

Revision History 

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