4YH2 | pdb_00004yh2

Glutathione Transferase E6 from Drosophila melanogaster

PDB DOI: https://doi.org/10.2210/pdb4YH2/pdb

Classification: TRANSFERASE
Organism(s): Drosophila melanogaster
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2015-02-26 Released: 2016-02-10
Deposition Author(s): Wongsantichon, J., Robinson, R.C., Ketterman, A.J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free:
0.188 (Depositor), 0.190 (DCC)
R-Value Work:
0.157 (Depositor)
R-Value Observed:
0.159 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Epsilon glutathione transferases possess a unique class-conserved subunit interface motif that directly interacts with glutathione in the active site

Wongsantichon, J., Robinson, R.C., Ketterman, A.J.

(2015) Biosci Rep 35

PubMed: 26487708 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1042/BSR20150183
Primary Citation Related Structures:
4YH2

PubMed Abstract:
Epsilon class glutathione transferases (GSTs) have been shown to contribute significantly to insecticide resistance. We report a new Epsilon class protein crystal structure from Drosophila melanogaster for the glutathione transferase DmGSTE6. The structure reveals a novel Epsilon clasp motif that is conserved across hundreds of millions of years of evolution of the insect Diptera order. This histidine-serine motif lies in the subunit interface and appears to contribute to quaternary stability as well as directly connecting the two glutathiones in the active sites of this dimeric enzyme.

Organizational Affiliation

Institute of Molecular and Cell Biology, A*STAR (Agency for Science, Technology and Research), Biopolis, Singapore 138673.

Macromolecule Content

Total Structure Weight: 101.4 kDa
Atom Count: 8,099
Modeled Residue Count: 881
Deposited Residue Count: 888
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S transferase E6	A, B, C, D	222	Drosophila melanogaster	Mutation(s): 0 Gene Names: GstE6, CG17530, Dmel_CG17530 EC: 2.5.1.18 (PDB Primary Data), 1.11.1.9 (UniProt)
UniProt
Find proteins for A1ZB71 (Drosophila melanogaster) Explore A1ZB71 Go to UniProtKB: A1ZB71
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	A1ZB71
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH Query on GSH Download:Ideal Coordinates CCD File SDF format, chain H [auth D] SDF format, chain G [auth C] SDF format, chain F [auth B] SDF format, chain E [auth A] MOL2 format, chain H [auth D] MOL2 format, chain G [auth C] MOL2 format, chain F [auth B] MOL2 format, chain E [auth A] mmCIF format, chain H [auth D] mmCIF format, chain G [auth C] mmCIF format, chain F [auth B] mmCIF format, chain E [auth A]	E [auth A], F [auth B], G [auth C], H [auth D]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Biologically Interesting Molecules (External Reference)

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_002593 (GSH) Query on PRD_002593	E [auth A], F [auth B], G [auth C], H [auth D]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D] Interactions & Density Focus chain E [auth A] Focus chain F [auth B] Focus chain G [auth C] Focus chain H [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.72 Å
R-Value Free: 0.188 (Depositor), 0.190 (DCC)
R-Value Work: 0.157 (Depositor)
R-Value Observed: 0.159 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 176.35	α = 90
b = 58.86	β = 128.25
c = 122.81	γ = 90

Software Package:

Software Name	Purpose
Aimless	data scaling
PHENIX	refinement
PDB_EXTRACT	data extraction
xia2	data reduction
xia2	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-02-10

Deposition Author(s):

Wongsantichon, J.

Robinson, R.C.

Ketterman, A.J.

Revision History (Full details and data files)

Version 1.0: 2016-02-10
Type: Initial release
Version 1.1: 2020-02-05
Changes: Data collection, Database references, Derived calculations
Version 1.2: 2024-03-20
Changes: Data collection, Database references