3QAW | pdb_00003qaw

Crystal structure of a glutathione-S-transferase from Antarctic clam Laternula elliptica in a complex with glutathione

• PDB DOI: https://doi.org/10.2210/pdb3QAW/pdb

• Classification: TRANSFERASE
• Organism(s): Laternula elliptica
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2011-01-12 Released: 2012-02-01 
• Deposition Author(s): Park, A.K., Moon, J.H., Chi, Y.M.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free: 
  0.215 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.181 (Depositor), 0.209 (DCC) 

Starting Model: experimental

Literature

The structure of a shellfish specific GST class glutathione S-transferase from antarctic bivalve Laternula elliptica reveals novel active site architecture.

Park, A.K., Moon, J.H., Jang, E.H., Park, H., Ahn, I.Y., Lee, K.S., Chi, Y.M.

(2013) Proteins 81: 531-537

• PubMed: 23152139 
• DOI: https://doi.org/10.1002/prot.24208
• Primary Citation Related Structures: 
  3QAV, 3QAW


• PubMed Abstract: 
  

  Glutathione-S-transferases have been identified in all the living species examined so far, yet little is known about their function in marine organisms. In a previous report, the recently identified GST from Antarctic bivalve Laternula elliptica (LeGST) was classified into the rho class GST, but there are several unique features of LeGST that may justify reclassification, which could represent specific shellfish GSTs. Here, we determined the crystal structure of LeGST, which is a shellfish specific class of GST. The structural analysis showed that the relatively open and wide hydrophobic H-site of the LeGST allows this GST to accommodate various substrates. These results suggest that the H-site of LeGST may be the result of adaptation to their environments as sedentary organisms.

---

Organizational Affiliation: 
• Division of Biotechnology, College of Life Sciences, Korea University, Seoul 136-713, 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: 28.29 kDa 
• Atom Count: 1,933 
• Modeled Residue Count: 219 
• Deposited Residue Count: 243 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Rho-class glutathione S-transferase	A	243	Laternula elliptica	Mutation(s): 0  EC: 2.5.1.18
UniProt
Find proteins for B9VX79 (Laternula elliptica) Explore B9VX79  Go to UniProtKB:  B9VX79

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	B [auth A]	Glutathione C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.20 Å
• R-Value Free:  0.215 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.181 (Depositor), 0.209 (DCC) 

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.393	α = 90
b = 57.611	β = 123.84
c = 55.449	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2012-02-01 
Deposition Author(s): Park, A.K., Moon, J.H., Chi, Y.M.

Revision History  

• Version 1.0: 2012-02-01
  Type: Initial release
  
• Version 1.1: 2013-02-13
  Changes: Database references
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description