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3gxp

Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5

Method: X-RAY DIFFRACTION Dmax: 100.0 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Alpha-galactosidase A

Homo sapiens

UniProt P06280

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Homooligomer Protein × 2 其他Polymer 5 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 32–429 Chain B； UniProt 32–429 Not recorded alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 4 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 crystallization conditions：VAPOR DIFFUSION；vapor diffusion Resolution 2.20 Å R-free 0.265

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 3GXP Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1R46 Structure of human alpha-galactosidase Deposited 2003-10-03 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 EDO 1,2-ETHANEDIOL × 4 X-RAY DIFFRACTION
X-ray crystallization conditions 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
Resolution 3.25 Å R-free 0.301
1R47 Structure of human alpha-galactosidase Deposited 2003-10-03 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded GAL beta-D-galactopyranose × 2 EDO 1,2-ETHANEDIOL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions 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
Resolution 3.45 Å R-free 0.321
3GXN Crystal structure of apo alpha-galactosidase A at pH 4.5 Deposited 2009-04-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded SO4 SULFATE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；vapor diffusion
Resolution 3.01 Å R-free 0.301
3GXT Crystal structure of alpha-galactosidase A at pH 4.5 complexed with 1-deoxygalactonijirimycin Deposited 2009-04-02 Different oligomeric state Different ligand/ion Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded SO4 SULFATE ION × 5 NOJ 1-DEOXYNOJIRIMYCIN × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION；vapor diffusion
Resolution 2.70 Å R-free 0.306
3HG2 Human alpha-galactosidase catalytic mechanism 1. Empty active site Deposited 2009-05-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.202
3HG3 Human alpha-galactosidase catalytic mechanism 2. Substrate bound Deposited 2009-05-13 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Mutation：D170A Mutation：D170A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 2PE NONAETHYLENE GLYCOL × 5 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Magnesium acetate, Sodium Cacodylate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 1.90 Å R-free 0.197
3HG4 Human alpha-galactosidase catalytic mechanism 3. Covalent intermediate Deposited 2009-05-13 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.30 Å R-free 0.221
3HG5 Human alpha-galactosidase catalytic mechanism 4. Product bound Deposited 2009-05-13 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；293 K；PEG4000, Ammonium Sulfate, Sodium Acetate, pH 4.6, vapor diffusion, hanging drop, temperature 293K
Resolution 2.30 Å R-free 0.227
3LX9 Interconversion of Human Lysosomal Enzyme Specificities Deposited 2010-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa） Fragment：UNP residues 32-429
Chain B 32–429（398 aa） Fragment：UNP residues 32-429
Mutation：E203S,L206A Mutation：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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.04 Å R-free 0.218
3LXA Interconversion of Human Lysosomal Enzyme Specificities Deposited 2010-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa） Fragment：UNP residues 32-429
Chain B 32–429（398 aa） Fragment：UNP residues 32-429
Mutation：E203S L206A Mutation：E203S L206A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GLA alpha-D-galactopyranose × 4 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, vapor diffusion, hanging drop, temperature 293K
Resolution 3.04 Å R-free 0.244
3LXB Interconversion of Human Lysosomal Enzyme Specificities Deposited 2010-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa） Fragment：UNP residues 32-429
Chain B 32–429（398 aa） Fragment：UNP residues 32-429
Mutation：E203S,L206A Mutation：E203S,L206A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 GOL GLYCEROL × 6 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.85 Å R-free 0.264
3LXC Interconversion of Human Lysosomal Enzyme Specificities Deposited 2010-02-25 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa） Fragment：UNP residues 32-429
Chain B 32–429（398 aa） Fragment：UNP residues 32-429
Mutation：E203S,L206A Mutation：E203S,L206A NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；PEG8000, Sodium Cacodylate, Magnesium Acetate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.35 Å R-free 0.237
3S5Y Pharmacological Chaperoning in Human alpha-Galactosidase Deposited 2011-05-23 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa） Fragment：UNP Residues 32-429
Chain B 32–429（398 aa） Fragment：UNP Residues 32-429
Not recorded 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 crystallization conditions 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
Resolution 2.10 Å R-free 0.230
3S5Z Pharmacological Chaperoning in Human alpha-Galactosidase Deposited 2011-05-23 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 5.1；293 K；PEG 8000, Sodium Cacodylate, Magnesium Chloride, pH 5.1, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.00 Å R-free 0.234
3TV8 Pharmacological Chaperoning in Human alpha-Galactosidase Deposited 2011-09-19 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa） Fragment：UNP Residues 32-429
Chain B 32–429（398 aa） Fragment：UNP Residues 32-429
Mutation：D170A Mutation：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 crystallization conditions 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
Resolution 2.64 Å R-free 0.239
4NXS Crystal structure of human alpha-galactosidase A in complex with 1-deoxygalactonojirimycin-pFPhT Deposited 2013-12-09 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions 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
Resolution 2.55 Å R-free 0.232
6IBK Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfamidate ME763 Deposited 2018-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate,
Resolution 1.99 Å R-free 0.244
6IBM Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclosulfate ME776 Deposited 2018-11-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate
Resolution 2.07 Å R-free 0.242
6IBR Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol epoxide LWA481 Deposited 2018-11-30 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate
Resolution 2.02 Å R-free 0.256
6IBT Crystal structure of human alpha-galactosidase A in complex with alpha-galactose configured cyclophellitol aziridine ME737 Deposited 2018-11-30 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 4000 (50%), sodium acetate (pH 4.6) and lithium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM NaOAc pH 4.5, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.5；293 K；100 mM NaOAc pH 4.5, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 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 Deposited 2023-07-26 Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Not recorded 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 crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；293 K；100 mM Tris-HCl buffer 7.2, 25% PEG4000 and 200 mM ammonium sulfate
Resolution 2.00 Å R-free 0.186
9AVS Human alpha-galactosidase A in complex with saposin B Deposited 2024-03-04 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 32–429（398 aa）
Chain B 32–429（398 aa）
Mutation：D170A Mutation：D170A SO4 SULFATE ION × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 X-RAY DIFFRACTION
X-ray crystallization conditions 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.
Resolution 3.53 Å R-free 0.265

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View Construct and Data Evidence
UniProt name AGAL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–398； UniProt 32–429 Author chain B； PDBConstruct 1–398； UniProt 32–429

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

SAXS profile for 3gxp

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3gxp
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3gxp
Deposition date deposition_date2009-04-02
Structure title titleCrystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5
Keywords keywordshydrolase, Disease mutation, Disulfide bond, Glycoprotein, Glycosidase, Lysosome, RNA editing; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier31.00 Å
Radius of gyration Rg (electron density) rg_electron30.11 Å
Forward intensity I(0) i0140714000.00
Molecular weight molecular_weight92765.0 kDa
Excluded volume excluded_volume115140 ų
Envelope volume envelope_volume136670 ų
Hydration-shell volume shell_volume37470 ų
Envelope diameter envelope_diameter104.3 Å
Shell Rg shell_rg37.49 Å
Envelope Rg envelope_rg30.25 Å
Shape Rg shape_rg30.09 Å
Total Rg total_rg30.76 Å
Total atoms total_atoms6509
Residues n_residues781
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax100.0 Å
Rg (real space) rg_real31.00 Å
Rg uncertainty (real space) rg_real_error0.67 Å
I(0) (real space) i0_real1.4070e+08
I(0) uncertainty (real space) i0_real_error2.2300e+06
Rg (reciprocal space) rg_reciprocal31.00 Å
I(0) (reciprocal space) i0_reciprocal140700000.0000
Solution quality estimate total_estimate0.8967
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary31.4 Å
Skewness Skewness skewness0.301
Kurtosis Kurtosis kurtosis-0.540
Angular range angular_range— – 0.2550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha38420000.0000
Real-space data points n_real_points52
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.934
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (9)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd3gxpa1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.1 — Amylase, catalytic domain
Domain ID domain_idd3gxpa2
Class classb — All beta proteins
Fold Fold foldb.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamilyb.71.1 — Glycosyl hydrolase domain
Family Family familyb.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain
Domain ID domain_idd3gxpb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.1 — TIM beta/alpha-barrel
Superfamily Superfamily superfamilyc.1.8 — (Trans)glycosidases
Family Family familyc.1.8.1 — Amylase, catalytic domain
Domain ID domain_idd3gxpb2
Class classb — All beta proteins
Fold Fold foldb.71 — Glycosyl hydrolase domain
Superfamily Superfamily superfamilyb.71.1 — Glycosyl hydrolase domain
Family Family familyb.71.1.1 — alpha-Amylases, C-terminal beta-sheet domain

CATH v4.4 (4 domains)

Domain ID domain_id3gxpA01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id3gxpA02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II
Domain ID domain_id3gxpB01
Class class3 — Alpha Beta
Architecture architecture20 — Alpha-Beta Barrel
Topology topology20 — TIM Barrel
Homologous superfamily homologous superfamily70 — Aldolase class I
Domain ID domain_id3gxpB02
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily1180 — Golgi alpha-mannosidase II
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8. Citations (1)

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9. Files and Curves (10)