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

Method: X-RAY DIFFRACTION D_max: 99.7 Å Quality: GOOD

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

Alpha-galactosidase A

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	Other combination Homooligomer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 32–429 Chain B； UniProt 32–429	Not recorded	;alpha-D-mannopyranose-(1-3)-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 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

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 8K7K	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 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 × 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 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 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；vapor diffusion	Resolution 3.01 Å R-free 0.301
3GXP Crystal structure of acid-alpha-galactosidase A complexed with galactose at pH 4.5 Deposited 2009-04-02	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 × 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
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 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 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 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 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）	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 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	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 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 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 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	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 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	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 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 × 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 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 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	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 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 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	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 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	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 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 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	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
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 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

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	8k7k
Deposition date deposition_date	2023-07-26
Structure title title	Crystal structure of human lysosomal alpha-galactosidase A in complex with (2R,3S,4R,5R)-2,5-bis(hydroxymethyl)-1-methylpyrrolidine-3,4-diol
Keywords keywords	alpha-galactosidase, glycosidase, iminosugar, HYDROLASE; HYDROLASE
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	30.90 Å
Radius of gyration Rg (electron density) rg_electron	30.02 Å
Forward intensity I(0) i0	137866000.00
Molecular weight molecular_weight	91977.0 kDa
Excluded volume excluded_volume	114240 Å³
Envelope volume envelope_volume	134720 Å³
Hydration-shell volume shell_volume	37134 Å³
Envelope diameter envelope_diameter	105.3 Å
Shell Rg shell_rg	37.35 Å
Envelope Rg envelope_rg	30.06 Å
Shape Rg shape_rg	30.01 Å
Total Rg total_rg	30.66 Å
Total atoms total_atoms	6456
Residues n_residues	782
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	99.7 Å
Rg (real space) rg_real	30.89 Å
Rg uncertainty (real space) rg_real_error	0.52 Å
I(0) (real space) i0_real	1.3790e+08
I(0) uncertainty (real space) i0_real_error	1.9870e+06
Rg (reciprocal space) rg_reciprocal	30.90 Å
I(0) (reciprocal space) i0_reciprocal	137900000.0000
Solution quality estimate total_estimate	0.8973
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	97.7 Å
Skewness Skewness skewness	0.293
Kurtosis Kurtosis kurtosis	-0.550
Angular range angular_range	— – 0.2550 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	35090000.0000
Real-space data points n_real_points	52
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.919; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.969; Smooth: 0.935

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Alpha-galactosidase A
Molecular weight formula_weight	45394.5 kDa
EC 编号 ec_number	3.2.1.22
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	7269

LDNGLARTPTMGWLHWERFMCNLDCQEEPDSCISEKLFMEMAELMVSEGWKDAGYEYLCIDDCWMAPQRDSEGRLQADPQRFPHGIRQLANYVHSKGLKLGIYADVGNKTCAGFPGSFGYYDIDAQTFADWGVDLLKFDGCYCDSLENLADGYKHMSLALNRTGRSIVYSCEWPLYMWPFQKPNYTEIRQYCNHWRNFADIDDSWKSIKSILDWTSFNQERIVDVAGPGGWNDPDMLVIGNFGLSWNQQVTQMALWAIMAAPLFMSNDLRHISPQAKALLQDKDVIAINQDPLGKQGYQLRQGDNFEVWERPLSGLAWAVAMINRQEIGGPRSYTIAVASLGKGVACNPACFITQLLPVKRKLGFYEWTSRLRSHINPTGTVLLQLENTMQMSLKDLL

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	Homo sapiens

Entity 2 Entity 2 branched

Description description	;alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose ;
Molecular weight formula_weight	748.7 kDa
Source method src_method	man
Copy count entity_count	2

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	(2~{R},3~{S},4~{R},5~{R})-2,5-bis(hydroxymethyl)-1-methyl-pyrrolidine-3,4-diol
Molecular weight formula_weight	177.2 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	787

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8. Citations (1)

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Unit-cell length a length_a	90.399 Å
Unit-cell length b length_b	90.399 Å
Unit-cell length c length_c	216.201 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 32 2 1
Space-group number int_tables_number	154
Crystal system crystal_system	trigonal

Resolution resolution	2.000 Å
Low-resolution limit resolution_low	29.590 Å
R factor r_factor	0.1535
R_work r_work	0.1525
R_free r_free	0.1864

fit	/app/data/saxs_computation/k7/8k7k/8k7k.fit
pddf	/app/data/pr_computation/k7/8k7k/8k7k.pr.out
profile	/app/data/saxs_computation/k7/8k7k/8k7k.dat