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. 蛋白身份与相关结构 Protein Identity & Related Structures

GLUTATHIONE S-TRANSFERASE A2

HOMO SAPIENS

当前结构中的状态

Assembly	聚集状态	构建体	突变与修饰	配体、离子与共同组分	实验方法与环境	结构质量
1	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 1–221 链 B； UniProt 1–221	突变：YES	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray结晶条件：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)	分辨率 2.10 Å R-free 0.321
2	蛋白同源多聚体同源多聚体蛋白 × 2 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 C； UniProt 1–221 链 D； UniProt 1–221	突变：YES	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray结晶条件：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)	分辨率 2.10 Å R-free 0.321

数据库中的同蛋白其他状态

以下每一行都是同一 UniProt 蛋白在另一个 PDB 条目中的 biological assembly， “相对当前条目”直接指出证据层面的不同；没有差异标签表示当前已读取字段一致。

其他 PDB	相对当前条目 4ACS	Assembly / 聚集状态	构建体	突变与修饰	配体、离子与非聚合物	实验方法与环境	结构质量
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 提交 1995-01-23	突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–221（221 aa）链 B 1–221（221 aa）	未记录	GTX S-HEXYLGLUTATHIONE × 2	X-RAY DIFFRACTION mmCIF 未提供已读取条件	分辨率 2.50 Å
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione 提交 2007-09-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–222（222 aa）链 B 1–222（222 aa）	未记录	ASD 4-ANDROSTENE-3-17-DIONE × 2	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.10 Å R-free 0.288
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione 提交 2007-09-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 C 1–222（222 aa）链 D 1–222（222 aa）	未记录	ASD 4-ANDROSTENE-3-17-DIONE × 2	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.10 Å R-free 0.288
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione 提交 2007-09-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 E 1–222（222 aa）链 F 1–222（222 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.10 Å R-free 0.288
2VCT Glutathione transferase A2-2 in complex with delta-4-andostrene-3-17- dione 提交 2007-09-27	构建体不同突变/修饰不同配体/离子不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 G 1–222（222 aa）链 H 1–222（222 aa）	未记录	未记录非水小分子	X-RAY DIFFRACTION X-ray结晶条件 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.	分辨率 2.10 Å R-free 0.288
2WJU Glutathione transferase A2-2 in complex with glutathione 提交 2009-05-29	构建体不同突变/修饰不同实验环境不同结构质量不同	Assembly 1 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 1–222（222 aa）链 B 1–222（222 aa）	未记录	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.30 Å R-free 0.297
2WJU Glutathione transferase A2-2 in complex with glutathione 提交 2009-05-29	构建体不同突变/修饰不同实验环境不同结构质量不同	Assembly 2 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 C 1–222（222 aa）链 D 1–222（222 aa）	未记录	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.30 Å R-free 0.297
2WJU Glutathione transferase A2-2 in complex with glutathione 提交 2009-05-29	构建体不同突变/修饰不同实验环境不同结构质量不同	Assembly 3 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 E 1–222（222 aa）链 F 1–222（222 aa）	未记录	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.30 Å R-free 0.297
2WJU Glutathione transferase A2-2 in complex with glutathione 提交 2009-05-29	构建体不同突变/修饰不同实验环境不同结构质量不同	Assembly 4 蛋白同源多聚体同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 G 1–222（222 aa）链 H 1–222（222 aa）	未记录	GSH Glutathione × 2	X-RAY DIFFRACTION X-ray结晶条件 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	分辨率 2.30 Å R-free 0.297

共 3 个其他 PDB 条目、9 个 assembly。打开独立比较页并筛选聚集状态

查看构建体与数据证据

UniProt名称	GSTA2_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–221； UniProt 1–221 作者链 B； PDB构建体 1–221； UniProt 1–221 作者链 C； PDB构建体 1–221； UniProt 1–221 作者链 D； PDB构建体 1–221； UniProt 1–221

页面优先展示蛋白身份、当前 assembly、共同组分、聚集状态和跨 PDB 结构链接。链映射与序列区间收在“数据证据”中；数据库内部编号、导入时间和 assembly 操作表达式仅用于维护，因此不在读者页面展示。

SAXS 散射曲线 SAXS Profile

P(r) 距离分布 P(r) Distribution

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

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2. 结构基本信息 2. Structure Basics

条目编号 entry_id	4acs
沉积日期 deposition_date	2011-12-19
结构标题 title	Crystal structure of mutant GST A2-2 with enhanced catalytic efficiency with azathioprine
关键词 keywords	TRANSFERASE, OXIDATION-REDUCTION; TRANSFERASE
实验方法 method	X-RAY DIFFRACTION

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3. SAXS 参数 (CRYSOL 理论计算) 3. SAXS Parameters (CRYSOL)

回转半径 Rg (Guinier) rg_guinier	35.87 Å
回转半径 Rg (电子) rg_electron	35.85 Å
零角强度 I(0) i0	146254000.00
分子量 molecular_weight	101610.0 kDa
排除体积 excluded_volume	129110 Å³
包络体积 envelope_volume	166500 Å³
水化壳体积 shell_volume	40552 Å³
包络直径 envelope_diameter	123.8 Å
壳层 Rg shell_rg	40.26 Å
包络 Rg envelope_rg	35.46 Å
形状 Rg shape_rg	35.84 Å
总 Rg total_rg	36.17 Å
总原子数 total_atoms	7150
残基数 n_residues	872
球谐函数阶数 n_harmonics	20
q 范围 q_range	— – 0.5000 Å⁻¹
数据点数 n_points	101
壳层类型 shell_type	directional
溶剂电子密度 solvent_density	0.3340 e/Å³
壳层衬度 contrast_shell	0.0300 e/Å³
CRYSOL 版本 crysol_version	4.1.3

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4. P(r) 距离分布 (GNOM 反演) 4. P(r) Analysis (GNOM)

最大尺寸 Dmax dmax	118.5 Å
Rg (实空间) rg_real	36.17 Å
Rg 误差 (实空间) rg_real_error	1.01 Å
I(0) (实空间) i0_real	1.4630e+08
I(0) 误差 (实空间) i0_real_error	2.3000e+06
Rg (倒空间) rg_reciprocal	35.99 Å
I(0) (倒空间) i0_reciprocal	146200000.0000
解质量估计 total_estimate	0.8105
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	1
主峰位置 r_peak_primary	32.3 Å
偏度 Skewness skewness	0.505
峰度 Kurtosis kurtosis	-0.532
角度范围 angular_range	— – 0.2200 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	97150000.0000
实空间数据点数 n_real_points	45
GNOM 版本 gnom_version	4.1.3
质量判据 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. 晶体学与实验 5. Crystallography & Experiment

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6. 实体与聚合物信息 Entities & Polymers (3)

实体 1 Entity 1 polymer

描述 description	GLUTATHIONE S-TRANSFERASE A2
分子量 formula_weight	25627.7 kDa
EC 编号 ec_number	2.5.1.18
突变 mutation	YES
来源方法 src_method	man
拷贝数 entity_count	4

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B,C,D
原子数 atom_count	7665

MAEKPKLHYSNIRGRMESIRWLLAAAGVEFEEKFIKSAEDLDKLRNDGYLMFQQVPMVEIDGMKLVQTRAILNYIASKYNLYGKDIKEKALIDMYIEGIADLGEMIGDLSFSQPEEQDAKLALIQEKTKNRYFPAFEKVLKSHGQDYLVGNKLSRADIHLVELLYYVEELDSSLISSFPLLKALKTRISNLPTVKKFLQPGSPRKPPMDEKSLEESRKIFRH

来源 Source

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

实体 2 Entity 2 non-polymer

描述 description	GLUTATHIONE
分子量 formula_weight	307.3 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 3 Entity 3 water

描述 description	water
分子量 formula_weight	18.0 kDa
来源方法 src_method	nat
拷贝数 entity_count	515

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7. 折叠分类 (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

结构域编号 domain_id	d4acsa1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.0 — automated matches

结构域编号 domain_id	d4acsa2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

结构域编号 domain_id	d4acsb1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.0 — automated matches

结构域编号 domain_id	d4acsb2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

结构域编号 domain_id	d4acsc1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.0 — automated matches

结构域编号 domain_id	d4acsc2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

结构域编号 domain_id	d4acsd1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.47 — Thioredoxin fold
超家族 Superfamily superfamily	c.47.1 — Thioredoxin-like
家族 Family family	c.47.1.0 — automated matches

结构域编号 domain_id	d4acsd2
类 Class class	a — All alpha proteins
折叠类型 Fold fold	a.45 — GST C-terminal domain-like
超家族 Superfamily superfamily	a.45.1 — GST C-terminal domain-like
家族 Family family	a.45.1.1 — Glutathione S-transferase (GST), C-terminal domain

CATH v4.4 (8 domains)

结构域编号 domain_id	4acsA01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	4acsA02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	4acsB01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	4acsB02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	4acsC01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	4acsC02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

结构域编号 domain_id	4acsD01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	40 — 3-Layer(aba) Sandwich
拓扑 Topology topology	30 — Glutaredoxin
同源超家族 H-superfamily homologous superfamily	10 — Glutaredoxin

结构域编号 domain_id	4acsD02
类 Class class	1 — Mainly Alpha
架构 Architecture architecture	20 — Up-down Bundle
拓扑 Topology topology	1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
同源超家族 H-superfamily homologous superfamily	10 —

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8. 引用文献 (1)

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晶胞边长 a length_a	48.660 Å
晶胞边长 b length_b	94.800 Å
晶胞边长 c length_c	113.720 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	92.77 °
晶胞夹角 γ angle_gamma	90.00 °
晶胞分子数 Z z_pdb	8

空间群 space_group	P 1 21 1
空间群编号 int_tables_number	4
晶系 crystal_system	—

分辨率 resolution	2.100 Å
最低分辨率 resolution_low	40.000 Å
R 因子 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