1G3M

CRYSTAL STRUCTURE OF HUMAN ESTROGEN SULFOTRANSFERASE IN COMPLEX WITH IN-ACTIVE COFACTOR PAP AND 3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 

Starting Model: experimental
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wwPDB Validation   3D Report Full Report


This is version 1.4 of the entry. See complete history


Literature

Crystallographic analysis of a hydroxylated polychlorinated biphenyl (OH-PCB) bound to the catalytic estrogen binding site of human estrogen sulfotransferase.

Shevtsov, S.Petrotchenko, E.V.Pedersen, L.C.Negishi, M.

(2003) Environ Health Perspect 111: 884-888

  • DOI: https://doi.org/10.1289/ehp.6056
  • Primary Citation of Related Structures:  
    1G3M

  • PubMed Abstract: 

    Certain hydroxylated polychlorinated biphenyls (OH-PCBs) inhibit the human estrogen sulfotransferase (hEST) at subnanomolar concentrations, suggesting a possible pathway for PCB toxicity due to environmental exposure in humans. To address the structural basis of the inhibition, we have determined the crystal structure of hEST in the presence of the sulfuryl donor product 3 -phosphoadenosine 5 -phosphate and the OH-PCB 4,4 -OH 3,5,3,5 -tetraCB. The OH-PCB binds in the estrogen binding site with the position of the first phenolic ring in an orientation similar to the phenolic ring of 17 beta-estradiol. Interestingly, the OH-PCB does not bind in a planar conformation, but rather with a 30-degree twist between the phenyl rings. The crystal structure of hEST with the OH-PCB bound gives physical evidence that certain OH-PCBs can mimic binding of estrogenic compounds in biological systems.


  • Organizational Affiliation

    Pharmacogenetic Section, Laboratory of Reproductive and Developmental Toxicology, National Institute of Environmental Health Sciences, National Institutes of Health, Research Triangle Park, North Carolina 27709, USA.


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
ESTROGEN SULFOTRANSFERASE
A, B
294Homo sapiensMutation(s): 0 
Gene Names: STE
EC: 2.8.2.4
UniProt & NIH Common Fund Data Resources
Find proteins for P49888 (Homo sapiens)
Explore P49888 
Go to UniProtKB:  P49888
PHAROS:  P49888
GTEx:  ENSG00000109193 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP49888
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
A3P
Query on A3P

Download Ideal Coordinates CCD File 
C [auth A],
I [auth B]
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
PCQ
Query on PCQ

Download Ideal Coordinates CCD File 
D [auth A],
J [auth B]
3,5,3',5'-TETRACHLORO-BIPHENYL-4,4'-DIOL
C12 H6 Cl4 O2
YCYDXOVJXVALHY-UHFFFAOYSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
F [auth A],
G [auth A],
H [auth A]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Binding Affinity Annotations 
IDSourceBinding Affinity
PCQ PDBBind:  1G3M IC50: 0.1 (nM) from 1 assay(s)
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.70 Å
  • R-Value Free: 0.219 
  • R-Value Work: 0.193 
  • R-Value Observed: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 62.687α = 90
b = 96.894β = 92.58
c = 61.724γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
CCP4model building
CNSrefinement
Omodel building
CCP4phasing
CNSphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2003-07-22
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2024-02-07
    Changes: Data collection, Database references, Derived calculations
  • Version 1.4: 2024-04-03
    Changes: Refinement description