7EBU

Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in Daidzein- and glutathione-bound form

PDB DOI: https://doi.org/10.2210/pdb7EBU/pdb

Classification: TRANSFERASE
Organism(s): Aedes aegypti
Expression System: Escherichia coli 'BL21-Gold(DE3)pLysS AG
Mutation(s): No

Deposited: 2021-03-11 Released: 2022-01-26
Deposition Author(s): Inaba, K., Koiwai, K., Senda, M., Senda, T., Niwa, R.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology (Japan), Japan Agency for Medical Research and Development (AMED)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.244
R-Value Work: 0.190
R-Value Observed: 0.193

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti.

Inaba, K., Ebihara, K., Senda, M., Yoshino, R., Sakuma, C., Koiwai, K., Takaya, D., Watanabe, C., Watanabe, A., Kawashima, Y., Fukuzawa, K., Imamura, R., Kojima, H., Okabe, T., Uemura, N., Kasai, S., Kanuka, H., Nishimura, T., Watanabe, K., Inoue, H., Fujikawa, Y., Honma, T., Hirokawa, T., Senda, T., Niwa, R.

(2022) BMC Biol 20: 43-43

PubMed: 35172816 Search on PubMedSearch on PubMed Central
DOI: https://doi.org/10.1186/s12915-022-01233-2
Primary Citation of Related Structures:
7EBT, 7EBU, 7EBV, 7EBW

PubMed Abstract:
Mosquito control is a crucial global issue for protecting the human community from mosquito-borne diseases. There is an urgent need for the development of selective and safe reagents for mosquito control. Flavonoids, a group of chemical substances with variable phenolic structures, such as daidzein, have been suggested as potential mosquito larvicides with less risk to the environment. However, the mode of mosquito larvicidal action of flavonoids has not been elucidated.

Organizational Affiliation

Graduate School of Life and Environmental Sciences, University of Tsukuba, 1-1-1 Tennodai, Tsukuba, Ibaraki, 305-8572, Japan.

Macromolecule Content

Total Structure Weight: 106.85 kDa
Atom Count: 7,680
Modelled Residue Count: 873
Deposited Residue Count: 908
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, C, D	227	Aedes aegypti	Mutation(s): 0 Gene Names: 5569853
UniProt
Find proteins for A0A1S4FIB3 (Aedes aegypti) Explore A0A1S4FIB3 Go to UniProtKB: A0A1S4FIB3
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1S4FIB3
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 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 E [auth A] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain O [auth D] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D]	E [auth A], J [auth B], M [auth C], O [auth D]	GLUTATHIONE C₁₀ H₁₇ N₃ O₆ S RWSXRVCMGQZWBV-WDSKDSINSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain M [auth C] Focus chain O [auth D]
ZF1 (Subject of Investigation/LOI) Query on ZF1 Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain P [auth D] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain P [auth D]	F [auth A], K [auth B], N [auth C], P [auth D]	7-hydroxy-3-(4-hydroxyphenyl)-4H-chromen-4-one C₁₅ H₁₀ O₄ ZQSIJRDFPHDXIC-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain P [auth D]
CA Query on CA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth B] SDF format, chain Q [auth D] SDF format, chain R [auth D] SDF format, chain S [auth D] SDF format, chain T [auth D] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth D] MOL2 format, chain S [auth D] MOL2 format, chain T [auth D]	G [auth A] H [auth A] I [auth A] L [auth B] Q [auth D] G [auth A], H [auth A], I [auth A], L [auth B], Q [auth D], R [auth D], S [auth D], T [auth D]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth B] Focus chain Q [auth D] Focus chain R [auth D] Focus chain S [auth D] Focus chain T [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.95 Å
R-Value Free: 0.244
R-Value Work: 0.190
R-Value Observed: 0.193
Space Group: I 4₁ 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 152.213	α = 90
b = 152.213	β = 90
c = 146.825	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2022-01-26

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	18K19163
Ministry of Education, Culture, Sports, Science and Technology (Japan)	Japan	25712010
Japan Agency for Medical Research and Development (AMED)	Japan	20am0101001

Revision History (Full details and data files)

Version 1.0: 2022-01-26
Type: Initial release
Version 1.1: 2022-04-13
Changes: Database references
Version 1.2: 2023-11-29
Changes: Data collection, Refinement description

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Help and Resources

7EBU

Crystal structure of Aedes aegypti Noppera-bo, glutathione S-transferase epsilon 8, in Daidzein- and glutathione-bound form

Molecular action of larvicidal flavonoids on ecdysteroidogenic glutathione S-transferase Noppera-bo in Aedes aegypti.

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)