4E8H | pdb_00004e8h

Structural of Bombyx mori glutathione transferase BmGSTD1 complex with GTT

• PDB DOI: https://doi.org/10.2210/pdb4E8H/pdb

• Classification: TRANSFERASE
• Organism(s): Bombyx mori
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-20 Released: 2013-04-24 
• Deposition Author(s): Tan, X., Ma, X.X., Hu, X.M., Chen, Q.M., Zhao, P., Xia, Q.Y., Zhou, C.Z.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free: 
  0.231 (Depositor), 0.229 (DCC) 
• R-Value Work: 
  0.195 (Depositor), 0.193 (DCC) 
• R-Value Observed: 
  0.196 (Depositor) 

Starting Model: experimental

Literature

Structural of Bombyx mori glutathione transferase BmGSTD1 complex with GTT

Tan, X., Ma, X.X., Hu, X.M., Chen, Q.M., Zhao, P., Xia, Q.Y., Zhou, C.Z.

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)

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 102.71 kDa 
• Atom Count: 7,546 
• Modeled Residue Count: 862 
• Deposited Residue Count: 876 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione S-transferase	A, B, C, D	219	Bombyx mori	Mutation(s): 0  Gene Names: BmGSTd1 EC: 2.5.1.18
UniProt
Find proteins for O61996 (Bombyx mori) Explore O61996  Go to UniProtKB:  O61996

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GSH	E [auth A], F [auth B], G [auth C], H [auth D]	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)	E [auth A], F [auth B], G [auth C], H [auth D]	Glutathione	Peptide-like / Oxidation-reduction

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.12 Å
• R-Value Free:  0.231 (Depositor), 0.229 (DCC) 
• R-Value Work:  0.195 (Depositor), 0.193 (DCC) 
• R-Value Observed: 0.196 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 57.109	α = 90
b = 90.818	β = 102.77
c = 87.015	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
AMoRE	phasing
REFMAC	refinement
HKL-2000	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-04-24 
Deposition Author(s): Tan, X., Ma, X.X., Hu, X.M., Chen, Q.M., Zhao, P., Xia, Q.Y., Zhou, C.Z.

Revision History  

• Version 1.0: 2013-04-24
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description