Crystal Structure Analysis of human Glutathione S-transferase with S-hexyl glutatione and glycerol at 1.3 Angstrom

Experimental Data Snapshot

  • Resolution: 1.30 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 

Starting Model: experimental
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This is version 1.4 of the entry. See complete history


1.3-A resolution structure of human glutathione S-transferase with S-hexyl glutathione bound reveals possible extended ligandin binding site.

Le Trong, I.Stenkamp, R.E.Ibarra, C.Atkins, W.M.Adman, E.T.

(2002) Proteins 48: 618-627

  • DOI: https://doi.org/10.1002/prot.10162
  • Primary Citation of Related Structures:  
    1K3L, 1K3O, 1K3Y

  • PubMed Abstract: 

    Cytosolic glutathione S-transferases (GSTs) play a critical role in xenobiotic binding and metabolism, as well as in modulation of oxidative stress. Here, the high-resolution X-ray crystal structures of homodimeric human GSTA1-1 in the apo form and in complex with S-hexyl glutathione (two data sets) are reported at 1.8, 1.5, and 1.3A respectively. At this level of resolution, distinct conformations of the alkyl chain of S-hexyl glutathione are observed, reflecting the nonspecific nature of the hydrophobic substrate binding site (H-site). Also, an extensive network of ordered water, including 75 discrete solvent molecules, traverses the open subunit-subunit interface and connects the glutathione binding sites in each subunit. In the highest-resolution structure, three glycerol moieties lie within this network and directly connect the amino termini of the glutathione molecules. A search for ligand binding sites with the docking program Molecular Operating Environment identified the ordered water network binding site, lined mainly with hydrophobic residues, suggesting an extended ligand binding surface for nonsubstrate ligands, the so-called ligandin site. Finally, detailed comparison of the structures reported here with previously published X-ray structures reveal a possible reaction coordinate for ligand-dependent conformational changes in the active site and the C-terminus.

  • Organizational Affiliation

    Department of Biological Structure, University of Washington, Seattle Washington 98195, USA.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
A, B
221Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P08263 (Homo sapiens)
Explore P08263 
Go to UniProtKB:  P08263
GTEx:  ENSG00000243955 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP08263
Sequence Annotations
  • Reference Sequence
Experimental Data & Validation

Experimental Data

  • Resolution: 1.30 Å
  • R-Value Free: 0.205 
  • R-Value Work: 0.137 
  • R-Value Observed: 0.137 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 99.38α = 90
b = 93.77β = 93.39
c = 51.627γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-10-30
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-01-31
    Changes: Advisory, Experimental preparation
  • Version 1.4: 2023-08-16
    Changes: Advisory, Data collection, Database references, Derived calculations, Refinement description