4acs

Crystal structure of mutant GST A2-2 with enhanced catalytic efficiency with azathioprine

Method: X-RAY DIFFRACTION D_max: 118.5 Å Quality: GOOD

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

GLUTATHIONE S-TRANSFERASE A2

HOMO SAPIENS

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 1–221 Chain B； UniProt 1–221	Mutation：YES	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；CRYSTALS WERE GROWN BY HANING DROP METHOD BY MIXING EQUAL VOLUMES (4 UL) OF PROTEIN (10 MG/ML)AND GLUTATHIONE S-CONJUGATE (5 MM) MIXTURE AND RESERVOIR SOLUTION CONTAINING 9-14% PEG 4000 AND 2 MM DTT IN 100 MM TRIS-HCL (PH 7.8) WITH ADDITIONAL OCTYL D-BETA- GLUCOPYRANOSIDE TO A FINAL CONCENTRATION OF 0.1% (W/V)	Resolution 2.10 Å R-free 0.321
2	Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 1–221 Chain D； UniProt 1–221	Mutation：YES	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.8；CRYSTALS WERE GROWN BY HANING DROP METHOD BY MIXING EQUAL VOLUMES (4 UL) OF PROTEIN (10 MG/ML)AND GLUTATHIONE S-CONJUGATE (5 MM) MIXTURE AND RESERVOIR SOLUTION CONTAINING 9-14% PEG 4000 AND 2 MM DTT IN 100 MM TRIS-HCL (PH 7.8) WITH ADDITIONAL OCTYL D-BETA- GLUCOPYRANOSIDE TO A FINAL CONCENTRATION OF 0.1% (W/V)	Resolution 2.10 Å R-free 0.321

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 4ACS	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AGS A SURFACE MUTANT (G82R) OF A HUMAN ALPHA-GLUTATHIONE S-TRANSFERASE SHOWS DECREASED THERMAL STABILITY AND A NEW MODE OF MOLECULAR ASSOCIATION IN THE CRYSTAL Deposited 1995-01-23	Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–221（221 aa） Chain B 1–221（221 aa）	Not recorded	GTX S-HEXYLGLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.50 Å
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione Deposited 2007-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–222（222 aa） Chain B 1–222（222 aa）	Not recorded	ASD 4-ANDROSTENE-3-17-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 20 MM ANDROSTENE DIONE.	Resolution 2.10 Å R-free 0.288
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione Deposited 2007-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–222（222 aa） Chain D 1–222（222 aa）	Not recorded	ASD 4-ANDROSTENE-3-17-DIONE × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 20 MM ANDROSTENE DIONE.	Resolution 2.10 Å R-free 0.288
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione Deposited 2007-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–222（222 aa） Chain F 1–222（222 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 20 MM ANDROSTENE DIONE.	Resolution 2.10 Å R-free 0.288
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione Deposited 2007-09-27	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–222（222 aa） Chain H 1–222（222 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.8；HANGING DROP VAPOUR TECHNIQUE WAS USED. 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WAS MIXED WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1UL OF 20 MM ANDROSTENE DIONE.	Resolution 2.10 Å R-free 0.288
2WJU Glutathione transferase A2-2 in complex with glutathione Deposited 2009-05-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–222（222 aa） Chain B 1–222（222 aa）	Not recorded	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；THE CRYSTALS WERE OBTAINED BY HANGING DROP VAPOUR TECHNIQUE BY MIXING 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1 UL OF 25 MM GLUTATHIONE	Resolution 2.30 Å R-free 0.297
2WJU Glutathione transferase A2-2 in complex with glutathione Deposited 2009-05-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 1–222（222 aa） Chain D 1–222（222 aa）	Not recorded	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；THE CRYSTALS WERE OBTAINED BY HANGING DROP VAPOUR TECHNIQUE BY MIXING 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1 UL OF 25 MM GLUTATHIONE	Resolution 2.30 Å R-free 0.297
2WJU Glutathione transferase A2-2 in complex with glutathione Deposited 2009-05-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 1–222（222 aa） Chain F 1–222（222 aa）	Not recorded	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；THE CRYSTALS WERE OBTAINED BY HANGING DROP VAPOUR TECHNIQUE BY MIXING 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1 UL OF 25 MM GLUTATHIONE	Resolution 2.30 Å R-free 0.297
2WJU Glutathione transferase A2-2 in complex with glutathione Deposited 2009-05-29	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 1–222（222 aa） Chain H 1–222（222 aa）	Not recorded	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；THE CRYSTALS WERE OBTAINED BY HANGING DROP VAPOUR TECHNIQUE BY MIXING 5 UL OF RESERVOIR SOLUTION [100 MM TRIS-HCL PH 7.8, 18% (V/V) PEG 4000, AND 2 MM DITHIOTHREITOL] WITH 5 UL OF PROTEIN SOLUTION (10 MG/ML IN 10 MM TRIS-HCL PH 7.8), 1UL OF 200 MM SPERMINE AND 1 UL OF 25 MM GLUTATHIONE	Resolution 2.30 Å R-free 0.297

3 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	GSTA2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–221； UniProt 1–221 Author chain B； PDBConstruct 1–221； UniProt 1–221 Author chain C； PDBConstruct 1–221； UniProt 1–221 Author chain D； PDBConstruct 1–221； UniProt 1–221

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

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	4acs
Deposition date deposition_date	2011-12-19
Structure title title	Crystal structure of mutant GST A2-2 with enhanced catalytic efficiency with azathioprine
Keywords keywords	TRANSFERASE, OXIDATION-REDUCTION; 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	35.87 Å
Radius of gyration Rg (electron density) rg_electron	35.85 Å
Forward intensity I(0) i0	146254000.00
Molecular weight molecular_weight	101610.0 kDa
Excluded volume excluded_volume	129110 Å³
Envelope volume envelope_volume	166500 Å³
Hydration-shell volume shell_volume	40552 Å³
Envelope diameter envelope_diameter	123.8 Å
Shell Rg shell_rg	40.26 Å
Envelope Rg envelope_rg	35.46 Å
Shape Rg shape_rg	35.84 Å
Total Rg total_rg	36.17 Å
Total atoms total_atoms	7150
Residues n_residues	872
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	118.5 Å
Rg (real space) rg_real	36.17 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.4630e+08
I(0) uncertainty (real space) i0_real_error	2.3000e+06
Rg (reciprocal space) rg_reciprocal	35.99 Å
I(0) (reciprocal space) i0_reciprocal	146200000.0000
Solution quality estimate total_estimate	0.8105
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	32.3 Å
Skewness Skewness skewness	0.505
Kurtosis Kurtosis kurtosis	-0.532
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	97150000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.665; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.818; Smooth: 0.720

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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 A2
Molecular weight formula_weight	25627.7 kDa
EC 编号 ec_number	2.5.1.18
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7665

MAEKPKLHYSNIRGRMESIRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKEKALIDMYIEGIADLGEMIGDLSFSQPEEQDAKLALIQEKTKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEESRKIFRH

来源 Source

来源生物 organism	HOMO SAPIENS
通用名 common_name	HUMAN
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	ESCHERICHIA COLI

Entity 2 Entity 2 non-polymer

Description description	GLUTATHIONE
Molecular weight formula_weight	307.3 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	515

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4acsa1
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.47.1.0 — automated matches

Domain ID domain_id	d4acsa2
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	d4acsb1
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.47.1.0 — automated matches

Domain ID domain_id	d4acsb2
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	d4acsc1
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.47.1.0 — automated matches

Domain ID domain_id	d4acsc2
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	d4acsd1
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.47.1.0 — automated matches

Domain ID domain_id	d4acsd2
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 (8 domains)

Domain ID domain_id	4acsA01
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	4acsA02
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	4acsB01
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	4acsB02
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	4acsC01
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	4acsC02
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	4acsD01
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	4acsD02
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	48.660 Å
Unit-cell length b length_b	94.800 Å
Unit-cell length c length_c	113.720 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	92.77 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	40.000 Å
R factor r_factor	0.2642
R_work r_work	0.2612
R_free r_free	0.3211

fit	/app/data/saxs_computation/ac/4acs/4acs.fit
pddf	/app/data/pr_computation/ac/4acs/4acs.pr.out
profile	/app/data/saxs_computation/ac/4acs/4acs.dat