2GWH | pdb_00002gwh

Human Sulfotranferase SULT1C2 in complex with PAP and pentachlorophenol


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.219 (Depositor), 0.236 (DCC) 
  • R-Value Work: 
    0.191 (Depositor), 0.209 (DCC) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Validation slider image for 2GWH

Ligand Structure Quality Assessment 


This is version 1.5 of the entry. See complete history

Literature

Structural and chemical profiling of the human cytosolic sulfotransferases.

Allali-Hassani, A.Pan, P.W.Dombrovski, L.Najmanovich, R.Tempel, W.Dong, A.Loppnau, P.Martin, F.Thornton, J.Thonton, J.Edwards, A.M.Bochkarev, A.Plotnikov, A.N.Vedadi, M.Arrowsmith, C.H.

(2007) PLoS Biol 5: e97-e97

  • DOI: https://doi.org/10.1371/journal.pbio.0050097
  • Primary Citation Related Structures: 
    1ZD1, 2AD1, 2GWH, 2H8K

  • PubMed Abstract: 

    The human cytosolic sulfotransfases (hSULTs) comprise a family of 12 phase II enzymes involved in the metabolism of drugs and hormones, the bioactivation of carcinogens, and the detoxification of xenobiotics. Knowledge of the structural and mechanistic basis of substrate specificity and activity is crucial for understanding steroid and hormone metabolism, drug sensitivity, pharmacogenomics, and response to environmental toxins. We have determined the crystal structures of five hSULTs for which structural information was lacking, and screened nine of the 12 hSULTs for binding and activity toward a panel of potential substrates and inhibitors, revealing unique "chemical fingerprints" for each protein. The family-wide analysis of the screening and structural data provides a comprehensive, high-level view of the determinants of substrate binding, the mechanisms of inhibition by substrates and environmental toxins, and the functions of the orphan family members SULT1C3 and SULT4A1. Evidence is provided for structural "priming" of the enzyme active site by cofactor binding, which influences the spectrum of small molecules that can bind to each enzyme. The data help explain substrate promiscuity in this family and, at the same time, reveal new similarities between hSULT family members that were previously unrecognized by sequence or structure comparison alone.


  • Organizational Affiliation
    • Structural Genomics Consortium, University of Toronto, Toronto, Ontario, Canada.

Macromolecule Content 

  • Total Structure Weight: 71.69 kDa 
  • Atom Count: 5,137 
  • Modeled Residue Count: 573 
  • Deposited Residue Count: 596 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Sulfotransferase 1C2
A, B
298Homo sapiensMutation(s): 0 
Gene Names: SULT1C2
EC: 2.8.2 (PDB Primary Data), 2.8.2.1 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for O75897 (Homo sapiens)
Explore O75897 
Go to UniProtKB:  O75897
PHAROS:  O75897
GTEx:  ENSG00000198075 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupO75897
Sequence Annotations
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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],
H [auth B]
ADENOSINE-3'-5'-DIPHOSPHATE
C10 H15 N5 O10 P2
WHTCPDAXWFLDIH-KQYNXXCUSA-N
PCI

Query on PCI



Download:Ideal Coordinates CCD File
D [auth A],
I [auth B],
J [auth B]
PENTACHLOROPHENOL
C6 H Cl5 O
IZUPBVBPLAPZRR-UHFFFAOYSA-N
UNX

Query on UNX



Download:Ideal Coordinates CCD File
E [auth A]
F [auth A]
G [auth A]
K [auth B]
L [auth B]
E [auth A],
F [auth A],
G [auth A],
K [auth B],
L [auth B],
M [auth B]
UNKNOWN ATOM OR ION
X

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.219 (Depositor), 0.236 (DCC) 
  • R-Value Work:  0.191 (Depositor), 0.209 (DCC) 
Space Group: I 4 2 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 135.216α = 90
b = 135.216β = 90
c = 158.072γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
REFMACrefinement
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

Revision History  (Full details and data files)

  • Version 1.0: 2006-05-16
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Advisory, Refinement description, Version format compliance
  • Version 1.3: 2017-10-18
    Changes: Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-06
    Changes: Structure summary