4L5L | pdb_00004l5l

Crystal structure of 26 kDa GST of Clonorchis sinensis in P212121 symmetry

• PDB DOI: https://doi.org/10.2210/pdb4L5L/pdb

• Classification: TRANSFERASE
• Organism(s): Clonorchis sinensis
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2013-06-11 Released: 2013-09-04 
• Deposition Author(s): Chung, Y.J., Han, Y.H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work: 
  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 
  0.180 (Depositor) 

Literature

Crystal structures of 26kDa Clonorchis sinensis glutathione S-transferase reveal zinc binding and putative metal binding.

Han, Y.H., Hong, S.J., Cheong, H.K., Chung, Y.J.

(2013) Biochem Biophys Res Commun 438: 457-461

• PubMed: 23916611 
• DOI: https://doi.org/10.1016/j.bbrc.2013.07.102
• Primary Citation Related Structures: 
  4L5L, 4L5O


• PubMed Abstract: 
  

  The crystal structures of CsGST in two different space groups revealed that Asp26 and His79 coordinate a zinc ion. In one space group, His46 of an adjacent molecule participates in the coordination within 2.0Å. In the other space group, Asp26, His79 and a water molecule coordinate a zinc ion. The CsGST-D26H structure showed that four histidine residues - His26 and His79 from one molecule and the same residues from a symmetry-related neighboring molecule - coordinate a zinc ion. The coordinated zinc ions are located between two molecules and mediate molecular contacts within the crystal.

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Organizational Affiliation: 
• Division of Magnetic Resonance Research, Korea Basic Science Institute (KBSI), Ochang, Chungbuk 363-883, Republic of Korea.

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: 51.27 kDa 
• Atom Count: 3,769 
• Modeled Residue Count: 434 
• Deposited Residue Count: 436 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Putative glutathione transferase	A, B	218	Clonorchis sinensis	Mutation(s): 0  EC: 2.5.1.18
UniProt
Find proteins for Q25595 (Clonorchis sinensis) Explore Q25595  Go to UniProtKB:  Q25595

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	C [auth A], F [auth B]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
MES	E [auth A], H [auth B]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.236 (Depositor), 0.235 (DCC) 
• R-Value Work:  0.177 (Depositor), 0.185 (DCC) 
• R-Value Observed: 0.180 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.272	α = 90
b = 67.455	β = 90
c = 120.701	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
MOLREP	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
HKL-2000	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-09-04 
Deposition Author(s): Chung, Y.J., Han, Y.H.

Revision History  

• Version 1.0: 2013-09-04
  Type: Initial release
  
• Version 1.1: 2017-11-15
  Changes: Refinement description
• Version 1.2: 2024-03-20
  Changes: Data collection, Database references, Derived calculations