5J4U | pdb_00005j4u

Crystal structure of a glutathione S-transferase PtGSTU30 from Populus trichocarpa in complex with GSH

PDB DOI: https://doi.org/10.2210/pdb5J4U/pdb

Classification: TRANSFERASE
Organism(s): Populus trichocarpa
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2016-04-01 Released: 2017-04-12
Deposition Author(s): Yang, Q., Gu, J., Yang, M., Zeng, Q.
Funding Organization(s): the Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free:
0.181 (Depositor), 0.185 (DCC)
R-Value Work:
0.170 (Depositor), 0.174 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

Validation slider image for 5J4U

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Functional and Structural Profiles of GST Gene Family from Three Populus Species Revealed the Sequence-function Decoupling of Orthologous Genes

Yang, Q., Han, X., Gu, J., Liu, Y., Yang, M., Zeng, Q.

To be published.

Macromolecule Content

Total Structure Weight: 27.16 kDa
Atom Count: 2,140
Modeled Residue Count: 218
Deposited Residue Count: 231
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutathione transferase family protein	A	231	Populus trichocarpa	Mutation(s): 0 Gene Names: POPTR_0011s14410g EC: 2.5.1.18
UniProt
Find proteins for B9I0G5 (Populus trichocarpa) Explore B9I0G5 Go to UniProtKB: B9I0G5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	B9I0G5
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 B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	Glutathione C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

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	B [auth A]	Glutathione	Peptide-like / Oxidation-reduction		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.25 Å
R-Value Free: 0.181 (Depositor), 0.185 (DCC)
R-Value Work: 0.170 (Depositor), 0.174 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 83.028	α = 90
b = 74.646	β = 121.87
c = 48.935	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
SCALEPACK	data scaling
PHASER	model building
PHENIX	refinement
PDB_EXTRACT	data extraction

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2017-04-12

Deposition Author(s):

Funding Organization	Location	Grant Number
the Natural Science Foundation of China	China	--

Revision History (Full details and data files)

Version 1.0: 2017-04-12
Type: Initial release
Version 1.1: 2023-11-08
Changes: Data collection, Database references, Refinement description

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.