3hg4

Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate

Method: X-RAY DIFFRACTION D_max: 100.0 Å Quality: GOOD

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

Alpha-galactosidase A

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	其他组合同源多聚体蛋白 × 2 其他聚合物 5 PDB 声明：dimeric（2）与蛋白拷贝数一致	链 A； UniProt 32–429 链 B； UniProt 32–429	未记录	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose × 2 ;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 7JZ 2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose × 2 SO4 SULFATE ION × 3 ACY ACETIC ACID × 4 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件：VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	分辨率 2.30 Å R-free 0.221

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 3HG4	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
1R46 Structure of human alpha-galactosidase 提交 2003-10-03	配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；30% PEG 4000, 0.1M TRIS HCL (PH 8.0), 0.2M AMMONIUM SULFATE, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 3.25 Å R-free 0.301
1R47 Structure of human alpha-galactosidase 提交 2003-10-03	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	GAL beta-D-galactopyranose × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；30% PEG 4000, 0.1M TRIS HCl, 0.2M AMMONIUM SULFATE, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	分辨率 3.45 Å R-free 0.321
3GXN Crystal structure of apo alpha-galactosidase A at pH 4.5 提交 2009-04-02	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；vapor diffusion	分辨率 3.01 Å R-free 0.301
3GXP Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5 提交 2009-04-02	配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	SO4 SULFATE ION × 4 GLA alpha-D-galactopyranose × 2 TAM TRIS(HYDROXYETHYL)AMINOMETHANE × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 MAN alpha-D-mannopyranose × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；vapor diffusion	分辨率 2.20 Å R-free 0.265
3GXT Crystal structure of alpha-galactosidase A at pH 4.5 complexed with 1-deoxygalactonijirimycin 提交 2009-04-02	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	SO4 SULFATE ION × 5 NOJ 1-DEOXYNOJIRIMYCIN × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION；vapor diffusion	分辨率 2.70 Å R-free 0.306
3HG2 Human alpha-galactosidase catalytic mechanism 1. Empty active site 提交 2009-05-13	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SO4 SULFATE ION × 3 ACY ACETIC ACID × 3 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.30 Å R-free 0.202
3HG3 Human alpha-galactosidase catalytic mechanism 2. Substrate bound 提交 2009-05-13	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 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	突变：D170A 突变：D170A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2PE NONAETHYLENE GLYCOL × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Magnesium acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 1.90 Å R-free 0.197
3HG5 Human alpha-galactosidase catalytic mechanism 4. Product bound 提交 2009-05-13	聚集状态不同配体/离子不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLA alpha-D-galactopyranose × 2 SO4 SULFATE ION × 4 ACY ACETIC ACID × 4 GAL beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	分辨率 2.30 Å R-free 0.227
3LX9 Interconversion of Human Lysosomal Enzyme Specificities 提交 2010-02-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）片段：UNP residues 32-429 链 B 32–429（398 aa）片段：UNP residues 32-429	突变：E203S,L206A 突变：E203S,L206A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 A2G 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.04 Å R-free 0.218
3LXA Interconversion of Human Lysosomal Enzyme Specificities 提交 2010-02-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）片段：UNP residues 32-429 链 B 32–429（398 aa）片段：UNP residues 32-429	突变：E203S L206A 突变：E203S L206A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLA alpha-D-galactopyranose × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, vapor diffusion, hanging drop, temperature 293K	分辨率 3.04 Å R-free 0.244
3LXB Interconversion of Human Lysosomal Enzyme Specificities 提交 2010-02-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）片段：UNP residues 32-429 链 B 32–429（398 aa）片段：UNP residues 32-429	突变：E203S,L206A 突变：E203S,L206A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.85 Å R-free 0.264
3LXC Interconversion of Human Lysosomal Enzyme Specificities 提交 2010-02-25	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）片段：UNP residues 32-429 链 B 32–429（398 aa）片段：UNP residues 32-429	突变：E203S,L206A 突变：E203S,L206A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.35 Å R-free 0.237
3S5Y Pharmacological Chaperoning in Human alpha-Galactosidase 提交 2011-05-23	构建体不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）片段：UNP Residues 32-429 链 B 32–429（398 aa）片段：UNP Residues 32-429	未记录	DGJ (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol × 2 2PE NONAETHYLENE GLYCOL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 1 ACY ACETIC ACID × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；8-15% PEG 8000, 0.1 M Sodium Cacodylate, 0.02 M Magnesium Chloride, pH 5.1, vapor diffusion, hanging drop, temperature 293K, VAPOR DIFFUSION, HANGING DROP	分辨率 2.10 Å R-free 0.230
3S5Z Pharmacological Chaperoning in Human alpha-Galactosidase 提交 2011-05-23	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	GLA alpha-D-galactopyranose × 2 GAL beta-D-galactopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；PEG 8000, Sodium Cacodylate, Magnesium Chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K	分辨率 2.00 Å R-free 0.234
3TV8 Pharmacological Chaperoning in Human alpha-Galactosidase 提交 2011-09-19	构建体不同突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）片段：UNP Residues 32-429 链 B 32–429（398 aa）片段：UNP Residues 32-429	突变：D170A 突变：D170A	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 3 2PE NONAETHYLENE GLYCOL × 3 DGJ (2R,3S,4R,5S)-2-(hydroxymethyl)piperidine-3,4,5-triol × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；20% PEG 4000, 200mM Ammonium Sulfate, 100mM Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K	分辨率 2.64 Å R-free 0.239
4NXS Crystal structure of human alpha-galactosidase A in complex with 1-deoxygalactonojirimycin-pFPhT 提交 2013-12-09	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	SO4 SULFATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2OZ (2R,3S,4R,5S)-N-(4-fluorophenyl)-3,4,5-trihydroxy-2-(hydroxymethyl)piperidine-1-carbothioamide × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；298 K；0.1 M acetate pH 4.5, 0.215 M ammonium sulfate, and 24% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 298K	分辨率 2.55 Å R-free 0.232
6IBK Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfamidate ME763 提交 2018-11-30	配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	ACT ACETATE ION × 3 SO4 SULFATE ION × 11 EDO 1,2-ETHANEDIOL × 12 YTW (3~{a}~{R},4~{S},5~{S},6~{S},7~{R},7~{a}~{S})-7-(hydroxymethyl)-2,2-bis(oxidanylidene)-3~{a},4,5,6,7,7~{a}-hexahydro-3~{H}-benzo[d][1,2,3]oxathiazole-4,5,6-triol × 2 PEG DI(HYDROXYETHYL)ETHER × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate,	分辨率 1.99 Å R-free 0.244
6IBM Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfate ME776 提交 2018-11-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	PEG DI(HYDROXYETHYL)ETHER × 2 ACT ACETATE ION × 4 SO4 SULFATE ION × 6 HF8 [(1~{S},2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-3,4,5,6-tetrakis(oxidanyl)cyclohexyl] hydrogen sulfate × 2 EDO 1,2-ETHANEDIOL × 18	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate	分辨率 2.07 Å R-free 0.242
6IBR Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol epoxide LWA481 提交 2018-11-30	配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	SO4 SULFATE ION × 7 EDO 1,2-ETHANEDIOL × 9 PEG DI(HYDROXYETHYL)ETHER × 4 ACT ACETATE ION × 6 HBE (2~{R},3~{S},4~{S},5~{R},6~{S})-5-(hydroxymethyl)-7-oxabicyclo[4.1.0]heptane-2,3,4-triol × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate	分辨率 2.02 Å R-free 0.256
6IBT Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol aziridine ME737 提交 2018-11-30	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 EDO 1,2-ETHANEDIOL × 7 PEG DI(HYDROXYETHYL)ETHER × 3 H9T (1~{S},2~{S},3~{S},4~{S},5~{R},6~{S})-5-(hydroxymethyl)-7-azabicyclo[4.1.0]heptane-2,3,4-triol × 2 SO4 SULFATE ION × 5 ACT ACETATE ION × 6	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate	分辨率 2.04 Å R-free 0.260
8K7D Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-(aminomethyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 VLN (2~{R},3~{R},4~{S},5~{R})-2-(aminomethyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 5	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM NaOAc pH 4.5, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.61 Å R-free 0.209
8K7E Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-(aminomethyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 VLN (2~{R},3~{R},4~{S},5~{R})-2-(aminomethyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.20 Å R-free 0.192
8K7F Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R,5R)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 VMF (2~{R},3~{R},4~{S},5~{R})-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM NaOAc pH 4.5, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 1.98 Å R-free 0.191
8K7G Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R,5R)-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 VMF (2~{R},3~{R},4~{S},5~{R})-2,5-bis(hydroxymethyl)pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.32 Å R-free 0.217
8K7H Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R)-2-(hydroxymethyl)-1-methylpyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 VMO (2~{R},3~{S},4~{R})-2-(hydroxymethyl)-1-methyl-pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.28 Å R-free 0.210
8K7I Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R,5R)-2-(hydroxymethyl)-5-((methylamino)methyl)pyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 VN0 (2~{R},3~{S},4~{R},5~{R})-2-(hydroxymethyl)-5-(methylaminomethyl)pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 5 P6G HEXAETHYLENE GLYCOL × 1 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.12 Å R-free 0.195
8K7J Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-((dimethylamino)methyl)-5-(hydroxymethyl)pyrrolidine-3,4-diol 提交 2023-07-26	配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 VNB (2~{R},3~{R},4~{S},5~{R})-2-[(dimethylamino)methyl]-5-(hydroxymethyl)pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 5 P6G HEXAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.01 Å R-free 0.191
8K7K Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R,5R)-2,5-bis(hydroxymethyl)-1-methylpyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 VNQ (2~{R},3~{S},4~{R},5~{R})-2,5-bis(hydroxymethyl)-1-methyl-pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 3	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.00 Å R-free 0.186
8K7L Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3R,4S,5R)-2-(aminomethyl)-5-(hydroxymethyl)-1-methylpyrrolidine-3,4-diol 提交 2023-07-26	聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合同源多聚体；蛋白 × 2 PDB 声明：dimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	未记录	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 VO0 (2~{R},3~{R},4~{S},5~{R})-2-(aminomethyl)-5-(hydroxymethyl)-1-methyl-pyrrolidine-3,4-diol × 2 SO4 SULFATE ION × 5 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate	分辨率 2.00 Å R-free 0.186
9AVS Human alpha-galactosidase A in complex with saposin B 提交 2024-03-04	突变/修饰不同聚集状态不同配体/离子不同实验环境不同结构质量不同	Assembly 1 其他组合异源复合物；蛋白 × 3 PDB 声明：trimeric	链 A 32–429（398 aa）链 B 32–429（398 aa）	突变：D170A 突变：D170A	SO4 SULFATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray结晶条件 VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；500 nL of protein (0.1 mM GLA plus 0.22 mM SapB) was mixed with 500 nL of reservoir solution (0.1 M Tris pH 8.0, 1 M Ammonium sulfate) and equilibrated against 70 uL reservoirs at 20 C.	分辨率 3.53 Å R-free 0.265

共 30 个其他 PDB 条目、30 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	AGAL_HUMAN
Isoform	—
PDB实体	1
链与序列区间	作者链 A； PDB构建体 1–398； UniProt 32–429 作者链 B； PDB构建体 1–398； UniProt 32–429

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	3hg4
沉积日期 deposition_date	2009-05-13
结构标题 title	Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate
关键词 keywords	;GLYCOPROTEIN, CARBOHYDRATE-BINDING PROTEIN, GLYCOSIDASE, LYSOSOMAL ENZYME, (BETA/ALPHA)8 BARREL, Disease mutation, Disulfide bond, Hydrolase, Lysosome ;; HYDROLASE
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	31.08 Å
回转半径 Rg (电子) rg_electron	30.24 Å
零角强度 I(0) i0	143036000.00
分子量 molecular_weight	93643.0 kDa
排除体积 excluded_volume	116240 Å³
包络体积 envelope_volume	139770 Å³
水化壳体积 shell_volume	38029 Å³
包络直径 envelope_diameter	105.2 Å
壳层 Rg shell_rg	37.72 Å
包络 Rg envelope_rg	30.45 Å
形状 Rg shape_rg	30.22 Å
总 Rg total_rg	30.91 Å
总原子数 total_atoms	6568
残基数 n_residues	782
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	100.0 Å
Rg (实空间) rg_real	31.07 Å
Rg 误差 (实空间) rg_real_error	0.61 Å
I(0) (实空间) i0_real	1.4300e+08
I(0) 误差 (实空间) i0_real_error	2.2540e+06
Rg (倒空间) rg_reciprocal	31.08 Å
I(0) (倒空间) i0_reciprocal	143000000.0000
解质量估计 total_estimate	0.8975
解质量评级 solution_quality	GOOD a GOOD solution
P(r) 峰数 n_peaks	2
主峰位置 r_peak_primary	33.4 Å
偏度 Skewness skewness	0.298
峰度 Kurtosis kurtosis	-0.534
角度范围 angular_range	— – 0.2550 Å⁻¹
当前正则化参数 α current_alpha	0.0000
最高正则化参数 α highest_alpha	41650000.0000
实空间数据点数 n_real_points	52
GNOM 版本 gnom_version	4.1.3
质量判据 quality_criteria	AN1: 0.000; Oscil: 0.922; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.971; Smooth: 0.927

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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 (10)

实体 1 Entity 1 polymer

描述 description	Alpha-galactosidase A
分子量 formula_weight	45394.5 kDa
EC 编号 ec_number	3.2.1.22
来源方法 src_method	man
拷贝数 entity_count	2

聚合物 Polymer

聚合物类型 type	polypeptide(L)
链编号 strand_id	A,B
原子数 atom_count	7250

LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL

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	Homo sapiens

实体 2 Entity 2 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	570.5 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 3 Entity 3 branched

描述 description	;alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
分子量 formula_weight	910.8 kDa
来源方法 src_method	man
拷贝数 entity_count	2

实体 4 Entity 4 branched

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	424.4 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 5 Entity 5 non-polymer

描述 description	2-deoxy-2,2-difluoro-beta-D-lyxo-hexopyranose
分子量 formula_weight	200.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	2

实体 6 Entity 6 non-polymer

描述 description	SULFATE ION
分子量 formula_weight	96.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	3

实体 7 Entity 7 non-polymer

描述 description	ACETIC ACID
分子量 formula_weight	60.1 kDa
来源方法 src_method	syn
拷贝数 entity_count	4

实体 8 Entity 8 non-polymer

描述 description	2-acetamido-2-deoxy-beta-D-glucopyranose
分子量 formula_weight	221.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 9 Entity 9 non-polymer

描述 description	beta-D-galactopyranose
分子量 formula_weight	180.2 kDa
来源方法 src_method	man
拷贝数 entity_count	1

实体 10 Entity 10 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	682

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7. 折叠分类 (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

结构域编号 domain_id	d3hg4a1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.1 — Amylase, catalytic domain

结构域编号 domain_id	d3hg4a2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

结构域编号 domain_id	d3hg4b1
类 Class class	c — Alpha and beta proteins (a/b)
折叠类型 Fold fold	c.1 — TIM beta/alpha-barrel
超家族 Superfamily superfamily	c.1.8 — (Trans)glycosidases
家族 Family family	c.1.8.1 — Amylase, catalytic domain

结构域编号 domain_id	d3hg4b2
类 Class class	b — All beta proteins
折叠类型 Fold fold	b.71 — Glycosyl hydrolase domain
超家族 Superfamily superfamily	b.71.1 — Glycosyl hydrolase domain
家族 Family family	b.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

CATH v4.4 (4 domains)

结构域编号 domain_id	3hg4A01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	3hg4A02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

结构域编号 domain_id	3hg4B01
类 Class class	3 — Alpha Beta
架构 Architecture architecture	20 — Alpha-Beta Barrel
拓扑 Topology topology	20 — TIM Barrel
同源超家族 H-superfamily homologous superfamily	70 — Aldolase class I

结构域编号 domain_id	3hg4B02
类 Class class	2 — Mainly Beta
架构 Architecture architecture	60 — Sandwich
拓扑 Topology topology	40 — Immunoglobulin-like
同源超家族 H-superfamily homologous superfamily	1180 — Golgi alpha-mannosidase II

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8. 引用文献 (1)

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晶胞边长 a length_a	90.218 Å
晶胞边长 b length_b	90.218 Å
晶胞边长 c length_c	216.615 Å
晶胞夹角 α angle_alpha	90.00 °
晶胞夹角 β angle_beta	90.00 °
晶胞夹角 γ angle_gamma	120.00 °
晶胞分子数 Z z_pdb	12

空间群 space_group	P 32 2 1
空间群编号 int_tables_number	154
晶系 crystal_system	—

分辨率 resolution	2.300 Å
最低分辨率 resolution_low	18.050 Å
R 因子 r_factor	0.1660
R_work r_work	0.1650
R_free r_free	0.2210

fit	/app/data/saxs_computation/hg/3hg4/3hg4.fit
pddf	/app/data/pr_computation/hg/3hg4/3hg4.pr.out
profile	/app/data/saxs_computation/hg/3hg4/3hg4.dat