1YJ6 | pdb_00001yj6

crystal structure of human glutathione S-transferase M1A-1A complexed with glutathionyl-zinc-trihydroxide

• PDB DOI: https://doi.org/10.2210/pdb1YJ6/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2005-01-13 Released: 2005-02-01 
• Deposition Author(s): Patskovsky, Y.V., Patskovska, L.N., Listowsky, I., Almo, S.C.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work: 
  0.230 (Depositor), 0.232 (DCC) 
• R-Value Observed: 
  0.230 (Depositor) 

Starting Model: experimental

Literature

Human Glutathione S-Transferase M1A-1A Catalyzes Formation of Gsh-Metal Complexes

Patskovsky, Y.V., Patskovska, L.N., Listowsky, I., Almo, S.C.

To be published.

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)

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 78.36 kDa 
• Atom Count: 5,581 
• Modeled Residue Count: 651 
• Deposited Residue Count: 654 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase Mu 1	A, B, C	218	Homo sapiens	Mutation(s): 0  Gene Names: GSTM1, GST1 EC: 2.5.1.18
UniProt & NIH Common Fund Data Resources
Find proteins for P09488 (Homo sapiens) Explore P09488  Go to UniProtKB:  P09488
PHAROS:  P09488 GTEx:  ENSG00000134184

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	E [auth A], G [auth B], I [auth C]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
ZN	D [auth A], F [auth B], H [auth C]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 3
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH)	E [auth A], G [auth B], I [auth C]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.264 (Depositor), 0.263 (DCC) 
• R-Value Work:  0.230 (Depositor), 0.232 (DCC) 
• R-Value Observed: 0.230 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 178.64	α = 90
b = 51.41	β = 122.47
c = 93.82	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
MOLREP	phasing
CNS	refinement
CCP4	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2005-02-01 
Deposition Author(s): Patskovsky, Y.V., Patskovska, L.N., Listowsky, I., Almo, S.C.

Revision History  

• Version 1.0: 2005-02-01
  Type: Initial release
  
• Version 1.1: 2008-04-30
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Version format compliance
• Version 1.3: 2017-10-11
  Changes: Refinement description
• Version 1.4: 2023-08-23
  Changes: Data collection, Database references, Derived calculations, Refinement description