5a4w

AtGSTF2 from Arabidopsis thaliana in complex with quercetrin

Method: X-RAY DIFFRACTION D_max: 106.1 Å Quality: GOOD

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

GLUTATHIONE S-TRANSFERASE F2

ARABIDOPSIS THALIANA

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–212 Chain B； UniProt 1–212 Chain C； UniProt 1–212 Chain D； UniProt 1–212 Chain E； UniProt 1–212 Chain F； UniProt 1–212	Not recorded	QCT 2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside × 8 ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray crystallization conditions：pH 7；0.1 M PTPC (PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE SYSTEM), 15% PEG 1.5K; 10 MG PER ML PROTEIN, pH 7	Resolution 2.25 Å R-free 0.242

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 5A4W	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BX9 GLUTATHIONE S-TRANSFERASE IN COMPLEX WITH HERBICIDE Deposited 1998-10-14	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 2–212（211 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.00	Resolution 2.60 Å R-free 0.248
1GNW STRUCTURE OF GLUTATHIONE S-TRANSFERASE Deposited 1996-09-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–211（211 aa） Chain B 1–211（211 aa）	Not recorded	GTX S-HEXYLGLUTATHIONE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.20 Å
5A4U AtGSTF2 from Arabidopsis thaliana in complex with indole-3-aldehyde Deposited 2015-06-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–212（212 aa） Chain B 1–212（212 aa） Chain C 1–212（212 aa） Chain D 1–212（212 aa） Chain E 1–212（212 aa） Chain F 1–212（212 aa）	Not recorded	I3A 1H-INDOLE-3-CARBALDEHYDE × 8 ACT ACETATE ION × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1M PCTP (PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE SYSTEM, 15% (W/V) PEG 1.5K PH 7.0. PROTEIN AT 10 MG PER ML	Resolution 2.00 Å R-free 0.234
5A4V AtGSTF2 from Arabidopsis thaliana in complex with quercetin Deposited 2015-06-15	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–212（212 aa） Chain B 1–212（212 aa） Chain C 1–212（212 aa） Chain D 1–212（212 aa） Chain E 1–212（212 aa） Chain F 1–212（212 aa）	Not recorded	ACT ACETATE ION × 6 QUE 3,5,7,3',4'-PENTAHYDROXYFLAVONE × 3	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.1 M PTCP (PROPIONIC ACID, CACODYLATE, BIS-TRIS PROPANE SYSTEM), 15% PEG 1.5K, PROTEIN AT 10 MG PER ML, pH 7	Resolution 2.38 Å R-free 0.245
5A5K AtGSTF2 from Arabidopsis thaliana in complex with camalexin Deposited 2015-06-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain C 1–212（212 aa） Chain K 1–212（212 aa） Chain M 1–212（212 aa） Chain P 1–212（212 aa） Chain R 1–212（212 aa） Chain T 1–212（212 aa）	Not recorded	7WB (2Z)-2-indol-3-ylidene-3H-1,3-thiazole × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2 M SODIUM ACETATE AND 20% (W/V) PEG 3350; PH 7.0; PROTEIN AT 10 MG PER ML	Resolution 2.77 Å R-free 0.284
5A5K AtGSTF2 from Arabidopsis thaliana in complex with camalexin Deposited 2015-06-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–212（212 aa） Chain B 1–212（212 aa） Chain I 1–212（212 aa） Chain J 1–212（212 aa） Chain L 1–212（212 aa） Chain S 1–212（212 aa）	Not recorded	7WB (2Z)-2-indol-3-ylidene-3H-1,3-thiazole × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2 M SODIUM ACETATE AND 20% (W/V) PEG 3350; PH 7.0; PROTEIN AT 10 MG PER ML	Resolution 2.77 Å R-free 0.284
5A5K AtGSTF2 from Arabidopsis thaliana in complex with camalexin Deposited 2015-06-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain E 1–212（212 aa） Chain O 1–212（212 aa） Chain U 1–212（212 aa） Chain V 1–212（212 aa） Chain W 1–212（212 aa） Chain X 1–212（212 aa）	Not recorded	7WB (2Z)-2-indol-3-ylidene-3H-1,3-thiazole × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2 M SODIUM ACETATE AND 20% (W/V) PEG 3350; PH 7.0; PROTEIN AT 10 MG PER ML	Resolution 2.77 Å R-free 0.284
5A5K AtGSTF2 from Arabidopsis thaliana in complex with camalexin Deposited 2015-06-18	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain D 1–212（212 aa） Chain F 1–212（212 aa） Chain G 1–212（212 aa） Chain H 1–212（212 aa） Chain N 1–212（212 aa） Chain Q 1–212（212 aa）	Not recorded	7WB (2Z)-2-indol-3-ylidene-3H-1,3-thiazole × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；0.2 M SODIUM ACETATE AND 20% (W/V) PEG 3350; PH 7.0; PROTEIN AT 10 MG PER ML	Resolution 2.77 Å R-free 0.284

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GSTF2_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–212； UniProt 1–212 Author chain B； PDBConstruct 1–212； UniProt 1–212 Author chain C； PDBConstruct 1–212； UniProt 1–212 Author chain D； PDBConstruct 1–212； UniProt 1–212 Author chain E； PDBConstruct 1–212； UniProt 1–212 Author chain F； PDBConstruct 1–212； UniProt 1–212

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5a4w
Deposition date deposition_date	2015-06-15
Structure title title	AtGSTF2 from Arabidopsis thaliana in complex with quercetrin
Keywords keywords	TRANSFERASE, GLUTATHIONE-S-TRANSFERASE, GST, PLANT, ARABIDOPSIS; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

▼

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.64 Å
Radius of gyration Rg (electron density) rg_electron	34.66 Å
Forward intensity I(0) i0	290801000.00
Molecular weight molecular_weight	141700.0 kDa
Excluded volume excluded_volume	178690 Å³
Envelope volume envelope_volume	222790 Å³
Hydration-shell volume shell_volume	52787 Å³
Envelope diameter envelope_diameter	106.4 Å
Shell Rg shell_rg	42.23 Å
Envelope Rg envelope_rg	33.55 Å
Shape Rg shape_rg	34.66 Å
Total Rg total_rg	35.21 Å
Total atoms total_atoms	10048
Residues n_residues	1258
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

▼

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	106.1 Å
Rg (real space) rg_real	35.44 Å
Rg uncertainty (real space) rg_real_error	0.73 Å
I(0) (real space) i0_real	2.9080e+08
I(0) uncertainty (real space) i0_real_error	4.7110e+06
Rg (reciprocal space) rg_reciprocal	35.57 Å
I(0) (reciprocal space) i0_reciprocal	290800000.0000
Solution quality estimate total_estimate	0.8377
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	45.8 Å
Skewness Skewness skewness	0.029
Kurtosis Kurtosis kurtosis	-0.772
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	156600000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.964; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.995; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	GLUTATHIONE S-TRANSFERASE F2
Molecular weight formula_weight	24162.6 kDa
EC 编号 ec_number	2.5.1.18
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	10395

MAGIKVFGHPASIATRRVLIALHEKNLDFELVHVELKDGEHKKEPFLSRNPFGQVPAFEDGDLKLFESRAITQYIAHRYENQGTNLLQTDSKNISQYAIMAIGMQVEDHQFDPVASKLAFEQIFKSIYGLTTDEAVVAEEEAKLAKVLDVYEARLKEFKYLAGETFTLTDLHHIPAIQYLLGTPTKKLFTERPRVNEWVAEITKRPASEKVQ

来源 Source

来源生物 organism	ARABIDOPSIS THALIANA
通用名 common_name	THALE CRESS
NCBI Class编号 ncbi_taxonomy_id	3702
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	2-(3,4-dihydroxyphenyl)-5,7-dihydroxy-4-oxo-4H-chromen-3-yl 6-deoxy-alpha-L-mannopyranoside
Molecular weight formula_weight	448.4 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 3 Entity 3 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	325

▼

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d5a4wa1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d5a4wa2
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d5a4wb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d5a4wb2
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d5a4wc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d5a4wc2
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d5a4wd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d5a4wd2
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d5a4we1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d5a4we2
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

Domain ID domain_id	d5a4wf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.47 — Thioredoxin fold
Superfamily Superfamily superfamily	c.47.1 — Thioredoxin-like
Family Family family	c.47.1.5 — Glutathione S-transferase (GST), N-terminal domain

Domain ID domain_id	d5a4wf2
Class class	a — All alpha proteins
Fold Fold fold	a.45 — GST C-terminal domain-like
Superfamily Superfamily superfamily	a.45.1 — GST C-terminal domain-like
Family Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id	5a4wA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5a4wA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5a4wB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5a4wB02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5a4wC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5a4wC02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5a4wD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5a4wD02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5a4wE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5a4wE02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

Domain ID domain_id	5a4wF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	5a4wF02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily	10 —

▶

8. Citations (1)

▶

Unit-cell length a length_a	87.350 Å
Unit-cell length b length_b	93.570 Å
Unit-cell length c length_c	152.420 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	59.090 Å
R factor r_factor	0.2089
R_work r_work	0.2072
R_free r_free	0.2419

fit	/app/data/saxs_computation/a4/5a4w/5a4w.fit
pddf	/app/data/pr_computation/a4/5a4w/5a4w.pr.out
profile	/app/data/saxs_computation/a4/5a4w/5a4w.dat