7DB2

Crystal structure of Drosophila melanogaster Noppera-bo, glutathione S-transferase epsilon 14 (DmGSTE14), in GS-dimedone-bound form

• PDB DOI: https://doi.org/10.2210/pdb7DB2/pdb

• Classification: TRANSFERASE
• Organism(s): Drosophila melanogaster
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): Yes 


• Deposited: 2020-10-18 Released: 2021-02-10 
• Deposition Author(s): Koiwai, K., Inaba, K., Yumoto, F., Senda, T., Niwa, R.
• Funding Organization(s): Japan Agency for Medical Research and Development (AMED), Japan Society for the Promotion of Science (JSPS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 

Starting Model: experimental

Literature

Non-steroidal inhibitors of Drosophila melanogaster steroidogenic glutathione S -transferase Noppera-bo

Koiwai, K., Morohashi, K., Inaba, K., Ebihara, K., Kojima, H., Okabe, T., Yoshino, R., Hirokawa, T., Nampo, T., Fujikawa, Y., Inoue, H., Yumoto, F., Senda, T., Niwa, R.

(2021) J Pestic Sci 46: 75-87

• DOI: https://doi.org/10.1584/jpestics.D20-072

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 Evidence: gel filtration

Macromolecule Content

• Total Structure Weight: 56.14 kDa 
• Atom Count: 4,254 
• Modelled Residue Count: 444 
• Deposited Residue Count: 478 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase E14	A, B	239	Drosophila melanogaster	Mutation(s): 1  Gene Names: GstE14, GSTD14-14, nobo, CG4688 EC: 2.5.1.18
UniProt
Find proteins for Q7JYX0 (Drosophila melanogaster) Explore Q7JYX0  Go to UniProtKB:  Q7JYX0

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH (Subject of Investigation/LOI)	D [auth A], G [auth B]	GLUTATHIONE C10 H17 N3 O6 S RWSXRVCMGQZWBV-WDSKDSINSA-N
DC1 (Subject of Investigation/LOI)	C [auth A], F [auth B]	5,5-DIMETHYLCYCLOHEXANE-1,3-DIONE C8 H12 O2 BADXJIPKFRBFOT-UHFFFAOYSA-N
DMS	E [auth A], H [auth B]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 0.219 
• R-Value Work: 0.195 
• R-Value Observed: 0.196 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 58.676	α = 90
b = 75.887	β = 90
c = 106.174	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2021-02-10 
Deposition Author(s): Koiwai, K., Inaba, K., Yumoto, F., Senda, T., Niwa, R.

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Funding Organization	Location	Grant Number
Japan Agency for Medical Research and Development (AMED)	Japan	18am0101113j0002
Japan Society for the Promotion of Science (JSPS)	Japan	15K14719
Japan Society for the Promotion of Science (JSPS)	Japan	18K19163

Revision History  

• Version 1.0: 2021-02-10
  Type: Initial release
  
• Version 1.1: 2021-03-31
  Changes: Database references
• Version 1.2: 2023-11-29
  Changes: Data collection, Database references, Refinement description