5YVO | pdb_00005yvo

Human Glutathione Transferase Omega1 covalently bound to ML175 inhibitor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free: 
    0.203 (Depositor), 0.215 (DCC) 
  • R-Value Work: 
    0.166 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 
    0.167 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 5YVO

Ligand Structure Quality Assessment 


This is version 2.1 of the entry. See complete history

Literature

Glutathione transferase Omega 1-1 (GSTO1-1) modulates Akt and MEK1/2 signaling in human neuroblastoma cell SH-SY5Y.

Saisawang, C.Wongsantichon, J.Robinson, R.C.Ketterman, A.J.

(2019) Proteins 87: 588-595

  • DOI: https://doi.org/10.1002/prot.25683
  • Primary Citation Related Structures: 
    5YVN, 5YVO

  • PubMed Abstract: 

    In the human neuroblastoma SH-SY5Y cell line, the glutathione transferase Omega 1-1 (GSTO1-1) appears to modulate Akt and MEK1/2 kinase activation. We observed a glutathionylation modification was involved in the activation of Akt but not MEK1/2. With the specific GSTO1-1 inhibitor ML175, we show the enzyme activity of GSTO1-1 is important for modulation as the inhibited GSTO1-1 allowed activation of both Akt and MEK1/2. The inhibition of GSTO1-1 showed a similar extent of activation of Akt and MEK1/2 as treatment by the endotoxin lipopolysaccharide. The GSTO1-1 also either directly interacts with Akt and MEK1/2 or interacts with a protein complexed with Akt and MEK1/2 as both kinases coimmunoprecipitated with GSTO1-1. The results suggest that GSTO1-1 enzyme activity inhibits the activation of these two kinases to maintain basal levels. The possible regulation by GSTO1-1 is of interest as both kinases have hundreds of potential downstream targets that are known to have contributions to various cellular processes including survival, growth, proliferation, and metabolism.


  • Organizational Affiliation
    • Institute of Molecular Biosciences, Mahidol University, Salaya, Nakhon Pathom, Thailand.

Macromolecule Content 

  • Total Structure Weight: 28.68 kDa 
  • Atom Count: 2,249 
  • Modeled Residue Count: 239 
  • Deposited Residue Count: 241 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Glutathione S-transferase omega-1241Homo sapiensMutation(s): 0 
Gene Names: GSTO1GSTTLP28
EC: 2.5.1.18 (PDB Primary Data), 1.8.5.1 (PDB Primary Data), 1.20.4.2 (PDB Primary Data)
UniProt & NIH Common Fund Data Resources
Find proteins for P78417 (Homo sapiens)
Explore P78417 
Go to UniProtKB:  P78417
PHAROS:  P78417
GTEx:  ENSG00000148834 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP78417
Sequence Annotations
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Reference Sequence

Small Molecules

Binding Affinity Annotations 
IDSourceBinding Affinity
MLX BindingDB:  5YVO IC50: 28 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.80 Å
  • R-Value Free:  0.203 (Depositor), 0.215 (DCC) 
  • R-Value Work:  0.166 (Depositor), 0.176 (DCC) 
  • R-Value Observed: 0.167 (Depositor) 
Space Group: P 31 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 56.744α = 90
b = 56.744β = 90
c = 139.356γ = 120
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History 

& Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Mahidol UniversityThailand--

Revision History  (Full details and data files)

  • Version 1.0: 2018-11-28
    Type: Initial release
  • Version 1.1: 2019-08-07
    Changes: Data collection, Database references
  • Version 2.0: 2022-04-13
    Changes: Database references, Non-polymer description, Structure summary
  • Version 2.1: 2024-11-06
    Changes: Data collection, Structure summary