8UDB | pdb_00008udb

Crystal Structure of Mu class GST from TuGSTm12 (Tetur05g05300) from Tetranychus urticae

PDB DOI: https://doi.org/10.2210/pdb8UDB/pdb

Classification: TRANSFERASE/SUBSTRATE
Organism(s): Tetranychus urticae
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-09-28 Released: 2025-03-19
Deposition Author(s): Khatri, K., Arriaza, R., Chruszcz, M.
Funding Organization(s): National Institute of Food and Agriculture (NIFA, United States)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free:
0.261 (Depositor), 0.266 (DCC)
R-Value Work:
0.215 (Depositor), 0.220 (DCC)

Starting Model: in silico
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Crystal Structure of mu class Glutathione-S-Transferease (GST) from Tetranychus urticae

Khatri, K., Ariazza, R., Chruszcz, M.

To be published.

Macromolecule Content

Total Structure Weight: 53.17 kDa
Atom Count: 3,712
Modeled Residue Count: 446
Deposited Residue Count: 450
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione-S-Transferase	A, B	225	Tetranychus urticae	Mutation(s): 0 Gene Names: 107360608 EC: 2.5.1.18
UniProt
Find proteins for T1K577 (Tetranychus urticae) Explore T1K577 Go to UniProtKB: T1K577
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	T1K577
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
GSH (Subject of Investigation/LOI) Query on GSH Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.75 Å
R-Value Free: 0.261 (Depositor), 0.266 (DCC)
R-Value Work: 0.215 (Depositor), 0.220 (DCC)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 60.464	α = 90
b = 60.464	β = 90
c = 234.998	γ = 120

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-3000	data reduction
HKL-3000	data scaling
MOLREP	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2025-03-19

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institute of Food and Agriculture (NIFA, United States)	United States	#2020-67014-31179

Revision History (Full details and data files)

Version 1.0: 2025-03-19
Type: Initial release

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.