3DD3

Crystal Structure of the Glutathione Transferase Pi enzyme in complex with the bifunctional inhibitor, Etharapta

• PDB DOI: https://doi.org/10.2210/pdb3DD3/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2008-06-05 Released: 2009-04-21 
• Deposition Author(s): Parker, L.J.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.260 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 

Literature

Rational design of an organometallic glutathione transferase inhibitor

Ang, W.H., Parker, L.J., De Luca, A., Juillerat-Jeanneret, L., Morton, C.J., Lo Bello, M., Parker, M.W., Dyson, P.J.

(2009) Angew Chem Int Ed Engl 48: 3854-3857

• PubMed: 19396894 
• DOI: https://doi.org/10.1002/anie.200900185
• Primary Citation of Related Structures:  
  3DD3, 3DGQ


• PubMed Abstract: 
  

  Double trouble: A hybrid organic-inorganic (organometallic) inhibitor was designed to target glutathione transferases. The metal center is used to direct protein binding, while the organic moiety acts as the active-site inhibitor (see picture). The mechanism of inhibition was studied using a range of biophysical and biochemical methods.

---

Organizational Affiliation: 

Institut des Sciences et Ingénierie Chimiques, Ecole Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 47.94 kDa 
• Atom Count: 3,422 
• Modelled Residue Count: 418 
• Deposited Residue Count: 420 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A, B	210	Homo sapiens	Mutation(s): 0  Gene Names: GSTP1 EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P09211 (Homo sapiens) Explore P09211  Go to UniProtKB:  P09211
PHAROS:  P09211 GTEx:  ENSG00000084207

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	E [auth A], G [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MES	C [auth A], F [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
RUC	D [auth A]	(eta6-benzene)ruthenium C6 H6 Ru BFWXATGPNNYZKL-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.25 Å
• R-Value Free: 0.260 
• R-Value Work: 0.200 
• R-Value Observed: 0.200 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.69	α = 90
b = 89.54	β = 97.81
c = 68.99	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection
MOSFLM	data reduction
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-04-21 
Deposition Author(s): Parker, L.J.

Revision History  

• Version 1.0: 2009-04-21
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2011-12-07
  Changes: Advisory, Non-polymer description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description