5DAK | pdb_00005dak

Crystal Structure of human Glutathione Transferase Pi complexed with a metalloid in the absence of Glutathione

• PDB DOI: https://doi.org/10.2210/pdb5DAK/pdb

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


• Deposited: 2015-08-20 Released: 2016-12-07 
• Deposition Author(s): Parker, L.J., Parker, M.W., Morton, C.J.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free: 
  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work: 
  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 
  0.159 (Depositor) 

Starting Model: experimental

Literature

Visualisation of Organoarsenic Human Glutathione Transferase P1-1 Complexes: Metabolism of Arsenic-based Therapeutics

Parker, L.J., Parker, M.W., Morton, C.J., Bocedi, A., Ascher, D.B., Aitken, J.B., Harris, H.H., Lo Bello, M., Ricci, G.

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)

Macromolecule Content 

• Total Structure Weight: 47.31 kDa 
• Atom Count: 3,287 
• Modeled Residue Count: 387 
• Deposited Residue Count: 420 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	A	210	Homo sapiens	Mutation(s): 0  Gene Names: GSTP1, FAEES3, GST3 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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase P	B	210	Homo sapiens	Mutation(s): 0  Gene Names: GSTP1, FAEES3, GST3 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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
MES	C [auth A], E [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ARS	D [auth A], F [auth B]	ARSENIC As RBFQJDQYXXHULB-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
CSO	B	L-PEPTIDE LINKING	C3 H7 N O3 S		CYS

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.11 Å
• R-Value Free:  0.204 (Depositor), 0.206 (DCC) 
• R-Value Work:  0.157 (Depositor), 0.159 (DCC) 
• R-Value Observed: 0.159 (Depositor) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 74.629	α = 90
b = 95.509	β = 98.26
c = 68.247	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
Aimless	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-12-07 
Deposition Author(s): Parker, L.J., Parker, M.W., Morton, C.J.

Revision History  

• Version 1.0: 2016-12-07
  Type: Initial release
  
• Version 1.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description
• Version 1.2: 2023-11-15
  Changes: Data collection
• Version 1.3: 2024-11-20
  Changes: Structure summary