SAXSdb — 1gnw

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

GLUTATHIONE S-TRANSFERASE

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 1–211 Chain B； UniProt 1–211	Not recorded	GTX S-HEXYLGLUTATHIONE × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 2.20 Å

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 1GNW	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
5A4U AtGSTF2 from Arabidopsis thaliana in complex with indole-3-aldehyde Deposited 2015-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 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 construct Different mutation/modification Different oligomeric state 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
5A4W AtGSTF2 from Arabidopsis thaliana in complex with quercetrin Deposited 2015-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 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	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
5A5K AtGSTF2 from Arabidopsis thaliana in complex with camalexin Deposited 2015-06-18	Different construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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 construct Different mutation/modification Different oligomeric state 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	GSTF4_ARATH
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–211； UniProt 1–211 Author chain B； PDBConstruct 1–211； UniProt 1–211

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1gnw
Deposition date deposition_date	1996-09-15
Structure title title	STRUCTURE OF GLUTATHIONE S-TRANSFERASE
Keywords keywords	TRANSFERASE, HERBICIDE DETOXIFICATION; TRANSFERASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	22.24 Å
Radius of gyration Rg (electron density) rg_electron	21.15 Å
Forward intensity I(0) i0	38152400.00
Molecular weight molecular_weight	49413.0 kDa
Excluded volume excluded_volume	62545 Å³
Envelope volume envelope_volume	71748 Å³
Hydration-shell volume shell_volume	27140 Å³
Envelope diameter envelope_diameter	64.4 Å
Shell Rg shell_rg	28.70 Å
Envelope Rg envelope_rg	21.20 Å
Shape Rg shape_rg	21.14 Å
Total Rg total_rg	22.07 Å
Total atoms total_atoms	4256
Residues n_residues	420
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

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

Maximum dimension Dmax dmax	63.9 Å
Rg (real space) rg_real	22.07 Å
Rg uncertainty (real space) rg_real_error	0.21 Å
I(0) (real space) i0_real	3.8150e+07
I(0) uncertainty (real space) i0_real_error	4.2250e+05
Rg (reciprocal space) rg_reciprocal	22.11 Å
I(0) (reciprocal space) i0_reciprocal	38150000.0000
Solution quality estimate total_estimate	0.9130
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	28.1 Å
Skewness Skewness skewness	0.050
Kurtosis Kurtosis kurtosis	-0.553
Angular range angular_range	— – 0.3550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8873000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.967; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.976; Smooth: 0.986

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	GLUTATHIONE S-TRANSFERASE
Molecular weight formula_weight	24031.4 kDa
EC 编号 ec_number	2.5.1.18
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	4916

AGIKVFGHPASIATRRVLIALHEKNLDFELVHVELKDGEHKKEPFLSRNPFGQVPAFEDGDLKLFESRAITQYIAHRYENQGTNLLQTDSKNISQYAIMAIGMQVEDHQFDPVASKLAFEQIFKSIYGLTTDEAVVAEEEAKLAKVLDVYEARLKEFKYLAGETFTLTDLHHIPAIQYLLGTPTKKLFTERPRVNEWVAEITKRPASEKVQ

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	S-HEXYLGLUTATHIONE
Molecular weight formula_weight	392.5 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	220

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1gnwa1
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	d1gnwa2
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	d1gnwb1
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	d1gnwb2
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

CATH v4.4 (4 domains)

Domain ID domain_id	1gnwA01
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	1gnwA02
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	1gnwB01
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	1gnwB02
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 —

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8. Citations (1)

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Unit-cell length a length_a	113.300 Å
Unit-cell length b length_b	113.300 Å
Unit-cell length c length_c	69.960 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 63
Space-group number int_tables_number	173
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	0.1750
R_work r_work	0.1750
R_free r_free	—

fit	/app/data/saxs_computation/gn/1gnw/1gnw.fit
pddf	/app/data/pr_computation/gn/1gnw/1gnw.pr.out
profile	/app/data/saxs_computation/gn/1gnw/1gnw.dat

STRUCTURE OF GLUTATHIONE S-TRANSFERASE

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

GLUTATHIONE S-TRANSFERASE

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution