8IX7

Functional significance of serine 13 in the active site of rice Phi-class glutathione S-transferase F3.

PDB DOI: https://doi.org/10.2210/pdb8IX7/pdb

Classification: PLANT PROTEIN
Organism(s): Oryza sativa Indica Group
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2023-03-31 Released: 2024-04-03
Deposition Author(s): Lee, W.C., Kong, K.H.
Funding Organization(s): National Research Foundation (NRF, Korea)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.207
R-Value Work: 0.181

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Functional significance of serine 13 in the active site of rice Phi-class glutathione S-transferase F3.

Im, J.K., Lee, W.C., Kong, J., Jo, H.J., Kong, K.H.

To be published.

Macromolecule Content

Total Structure Weight: 50.08 kDa
Atom Count: 3,887
Modelled Residue Count: 435
Deposited Residue Count: 442
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
glutathione transferase	A, B	221	Oryza sativa Indica Group	Mutation(s): 0 Gene Names: Plk1
UniProt
Find proteins for A2XC69 (Oryza sativa subsp. indica) Explore A2XC69 Go to UniProtKB: A2XC69
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A2XC69
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 C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B]	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: 1.70 Å
R-Value Free: 0.207
R-Value Work: 0.181
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 55.96	α = 90
b = 48.12	β = 102.33
c = 80.34	γ = 90

Software Package:

Software Name	Purpose
Blu-Ice	data collection
DENZO	data reduction
MOLREP	phasing
CNS	refinement
PDB_EXTRACT	data extraction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2024-04-03

Deposition Author(s):

Funding Organization	Location	Grant Number
National Research Foundation (NRF, Korea)	Korea, Republic Of	2018R1D1A1B07043467

Revision History (Full details and data files)

Version 1.0: 2024-04-03
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 R01GM133198.