1K3L

Crystal Structure Analysis of S-hexyl-glutathione Complex of Glutathione Transferase at 1.5 Angstroms Resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.158 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

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: 10.1002/prot.10162
  • Primary Citation of Related Structures:  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 i ...

    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.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
GLUTATHIONE S-TRANSFERASE A1
A, B
221Homo sapiensGene Names: GSTA1
EC: 2.5.1.18
Find proteins for P08263 (Homo sapiens)
Go to Gene View: GSTA1
Go to UniProtKB:  P08263
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
GTX
Query on GTX

Download SDF File 
Download CCD File 
A, B
S-HEXYLGLUTATHIONE
C16 H30 N3 O6 S
HXJDWCWJDCOHDG-RYUDHWBXSA-O
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.5 Å
  • R-Value Free: 0.241 
  • R-Value Work: 0.158 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 99.960α = 90.00
b = 93.994β = 92.63
c = 51.872γ = 90.00
Software Package:
Software NamePurpose
SHELXmodel building
SHELXphasing
SHELXL-97refinement
DENZOdata reduction
SCALEPACKdata scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-10-23
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance