3ap4

Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose

Method: X-RAY DIFFRACTION D_max: 90.5 Å Quality: EXCELLENT

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

Galectin-8

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 Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1–154	Fragment：N-terminal carbohydrate recognition domain	beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.33 Å R-free 0.251
2	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1–154	Fragment：N-terminal carbohydrate recognition domain	beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.33 Å R-free 0.251
3	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1–154	Fragment：N-terminal carbohydrate recognition domain	beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.33 Å R-free 0.251
4	Other combination Monomer Protein × 1 其他Polymer 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1–154	Fragment：N-terminal carbohydrate recognition domain	beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 2.33 Å R-free 0.251

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 3AP4	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2YRO Solution structure of the C-terminal Gal-bind lectin protein from Human Galectin-8 Deposited 2007-04-02	Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 175–316（142 aa） Fragment：Gal-bind_lectin domain	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient NMR sample composition 1.28mM Gal-binding lectin U-15N, 13C; 20mM d-Tris-HCl(pH 7.0); 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 90% H2O, 10% D2O \| 90% H2O/10% D2O	Resolution not provided
3AP5 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain Deposited 2010-10-11	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% PEG 3350 , pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.92 Å R-free 0.237
3AP6 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose 3'-sulfate Deposited 2010-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose 3'-sulfate, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 9% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.58 Å R-free 0.242
3AP6 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose 3'-sulfate Deposited 2010-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose 3'-sulfate, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 9% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.58 Å R-free 0.242
3AP6 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose 3'-sulfate Deposited 2010-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose 3'-sulfate, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 9% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.58 Å R-free 0.242
3AP6 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose 3'-sulfate Deposited 2010-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose 3'-sulfate, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 9% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.58 Å R-free 0.242
3AP7 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose sialic acid Deposited 2010-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM lactose sialic acid, 50mM sodium chloride, 0.5mM DTT, 80mM ammonium fluoride, 7.5% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.53 Å R-free 0.188
3AP9 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with Lacto-N-fucopentaose III Deposited 2010-10-12	Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.275mM protein, 10mM Hepes-NaOH, 2.75mM Lacto-N-fucopentaose III, 50mM sodium chloride, 0.5mM DTT, 50mM ammonium fluoride, 12% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.33 Å R-free 0.178
3APB Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with iodide Deposited 2010-10-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	IOD IODIDE ION × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.55mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.95 Å R-free 0.242
3APB Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with iodide Deposited 2010-10-14	Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–154（154 aa） Fragment：N-terminal carbohydrate recognition domain	Not recorded	IOD IODIDE ION × 16	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293.15 K；0.55mM protein, 10mM Hepes-NaOH, 50mM sodium chloride, 0.5mM DTT, 125mM ammonium fluoride, 8% PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.15K	Resolution 1.95 Å R-free 0.242
3OJB Crystal structure of C-terminal domain of human galectin-8 Deposited 2010-08-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 186–315（130 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；27.5% PEG 8000, 0.2M ammonium phosphate, 6.5% Ethylene Glycol, 0.1M Na Cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.01 Å R-free 0.292
3OJB Crystal structure of C-terminal domain of human galectin-8 Deposited 2010-08-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 186–315（130 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；27.5% PEG 8000, 0.2M ammonium phosphate, 6.5% Ethylene Glycol, 0.1M Na Cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.01 Å R-free 0.292
3OJB Crystal structure of C-terminal domain of human galectin-8 Deposited 2010-08-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 186–315（130 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；27.5% PEG 8000, 0.2M ammonium phosphate, 6.5% Ethylene Glycol, 0.1M Na Cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.01 Å R-free 0.292
3OJB Crystal structure of C-terminal domain of human galectin-8 Deposited 2010-08-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 186–315（130 aa） Fragment：C-terminal domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；281 K；27.5% PEG 8000, 0.2M ammonium phosphate, 6.5% Ethylene Glycol, 0.1M Na Cacodylate, VAPOR DIFFUSION, HANGING DROP, temperature 281K	Resolution 3.01 Å R-free 0.292
3VKL Protease-resistant mutant form of human Galectin-8 in complex with two lactose molecules Deposited 2011-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain Chain A 184–317（134 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain	Not recorded	EDO 1,2-ETHANEDIOL × 12	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；2-3%(v/v) 1,4-dioxane, 9-10%(w/v) PEG20000, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.264
3VKL Protease-resistant mutant form of human Galectin-8 in complex with two lactose molecules Deposited 2011-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–155（155 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain Chain B 184–317（134 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain	Not recorded	EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；2-3%(v/v) 1,4-dioxane, 9-10%(w/v) PEG20000, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.55 Å R-free 0.264
3VKM Protease-resistant mutant form of Human Galectin-8 in complex with sialyllactose and lactose Deposited 2011-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain Chain A 184–317（134 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain	Not recorded	EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；2-3%(v/v) 1,4-dioxane, 9-10%(w/v) PEG20000, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.98 Å R-free 0.261
3VKM Protease-resistant mutant form of Human Galectin-8 in complex with sialyllactose and lactose Deposited 2011-11-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–155（155 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain Chain B 184–317（134 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain	Not recorded	EDO 1,2-ETHANEDIOL × 13	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；2-3%(v/v) 1,4-dioxane, 9-10%(w/v) PEG20000, 0.1M bicine, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.98 Å R-free 0.261
3VKN Galectin-8 N-terminal domain in free form Deposited 2011-11-18	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–153（153 aa） Fragment：N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；30%(v/v) PEG 400, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.98 Å R-free 0.251
3VKN Galectin-8 N-terminal domain in free form Deposited 2011-11-18	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–153（153 aa） Fragment：N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；30%(v/v) PEG 400, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 1.98 Å R-free 0.251
3VKO Galectin-8 N-terminal domain in complex with sialyllactosamine Deposited 2011-11-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–153（153 aa） Fragment：N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；30%(v/v) PEG400, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.08 Å R-free 0.249
3VKO Galectin-8 N-terminal domain in complex with sialyllactosamine Deposited 2011-11-18	Different construct Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–153（153 aa） Fragment：N-TERMINAL CARBOHYDRATE RECOGNITION DOMAIN	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；293 K；30%(v/v) PEG400, 0.1M CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 2.08 Å R-free 0.249
4BMB Crystal structure of the N terminal domain of human Galectin 8 Deposited 2013-05-07	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–153（150 aa） Fragment：N TERMINAL DOMAIN, RESIDUES 4-153	Not recorded	ZN ZINC ION × 1 NA SODIUM ION × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions 20% W/V PEG 4000, 100 MM HEPES SODIUM SALT (PH 7.2) AND 10 MM ZINC CHLORIDE	Resolution 1.35 Å R-free 0.177
4BME Crystal structure of the N terminal domain of human Galectin 8, F19Y mutant Deposited 2013-05-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–155（152 aa） Fragment：N TERMINAL DOMAIN, RESIDUES 4-155	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 30% W/V PEG 4000, 100 MM MES SODIUM SALT (PH 6.5)	Resolution 2.00 Å R-free 0.241
4BME Crystal structure of the N terminal domain of human Galectin 8, F19Y mutant Deposited 2013-05-07	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain B 4–155（152 aa） Fragment：N TERMINAL DOMAIN, RESIDUES 4-155	Mutation：YES	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 30% W/V PEG 4000, 100 MM MES SODIUM SALT (PH 6.5)	Resolution 2.00 Å R-free 0.241
4FQZ Crystal structure of a protease-resistant mutant form of human galectin-8 Deposited 2012-06-26	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain Chain A 184–317（134 aa） Fragment：N-terminal carbohydrate recognition domain, C-terminal carbohydrate recognition domain	Not recorded	EDO 1,2-ETHANEDIOL × 10	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 9；293 K；10% PEG 20000, 0.1M Bicine, 2% Dioxane, pH 9.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.80 Å R-free 0.253
4GXL The crystal structure of Galectin-8 C-CRD in complex with NDP52 Deposited 2012-09-04	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 186–317（132 aa） Fragment：UNP residues 186-317	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.5；283 K；2% PEG 400, 0.1M HEPES sodium pH 7.5, 2.0M ammonium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 283K	Resolution 2.02 Å R-free 0.216
4HAN Crystal structure of Galectin 8 with NDP52 peptide Deposited 2012-09-27	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–155（155 aa） Fragment：UNP residues 1-155. 184-317 Chain A 184–317（134 aa） Fragment：UNP residues 1-155. 184-317 Chain B 1–155（155 aa） Fragment：UNP residues 1-155. 184-317 Chain B 184–317（134 aa） Fragment：UNP residues 1-155. 184-317	Not recorded	NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 2 PEG DI(HYDROXYETHYL)ETHER × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；295 K；0.1M Tris-Hcl pH8.5, 30~34% (v/w) PEG400, 200mM LiSO4, and 10mM Nicotinamide adenine dinucleotide, VAPOR DIFFUSION, HANGING DROP, temperature 295K	Resolution 2.55 Å R-free 0.214
5GZC Crystal structure of Galectin-8 N-CRD with part of linker Deposited 2016-09-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–158（152 aa） Fragment：carbohydrate recognition domain (UNP RESIDUES 7-158)	Not recorded	GOL GLYCEROL × 1 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 2000MME	Resolution 1.08 Å R-free 0.163
5GZD Galectin-8 N-terminal domain carbohydrate recognition domain Deposited 2016-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–154（148 aa） Fragment：carbohydrate recognition domain (UNP RESIDUES 7-154)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 2000MME	Resolution 1.19 Å R-free 0.212
5GZE Galectin-8 N-terminal domain carbohydrate recognition domain Deposited 2016-09-28	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–154（148 aa） Fragment：carbohydrate recognition domain (UNP RESIDUES 7-154)	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；PEG 2000MME	Resolution 1.32 Å R-free 0.278
5GZF Galectin-8 N-terminal domain carbohydrate recognition domain Deposited 2016-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–186（186 aa） Fragment：carbohydrate recognition domain (UNP RESIDUES 1-186)	Not recorded	NA SODIUM ION × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；298 K；0.1M Tris pH 8.5, 0.01M NiCl2, 20% (W/V) PEG 2000 MME	Resolution 2.00 Å R-free 0.218
5GZG Galectin-8 N-terminal domain carbohydrate recognition domain Deposited 2016-09-28	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–186（186 aa） Fragment：carbohydrate recognition domain (UNP RESIDUES 1-186)	Not recorded	NA SODIUM ION × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；0.1M Tris pH 8.5, 0.01M NiCl2,20% (W/V) PEG2000 MME	Resolution 2.00 Å R-free 0.258
5T7I Crystal structure of galectin-8N in complex with LNnT Deposited 2016-09-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal Domaine (UNP residues 1-155)	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate	Resolution 2.00 Å R-free 0.217
5T7S Crystal structure of galectin-8N in complex with Lactose Deposited 2016-09-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal Domaine (UNP residues 1-155)	Mutation：M56V Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate	Resolution 1.90 Å R-free 0.180
5T7T Galectin-8 N terminal domain in complex with LNT Deposited 2016-09-05	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal Domaine (UNP residues 1-155)	Mutation：M56V Non-standard monomer：Yes (specific site not provided by mmCIF)	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate	Resolution 1.96 Å R-free 0.215
5T7U Crystal structure of galectin-8N in complex with Glycerol Deposited 2016-09-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal Domaine (UNP residues 1-155)	Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2 NA SODIUM ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate	Resolution 1.58 Å R-free 0.147
5VWG Galectin-8 N terminal domain in complex with Methyl 3-O-[1-carboxyethyl]-beta-D-galactopyranoside Deposited 2017-05-21	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–155（155 aa） Fragment：N-terminal domain (UNP residues 1-155)	Mutation：M56V Non-standard monomer：Yes (specific site not provided by mmCIF)	9QG methyl 3-O-[(1R)-1-carboxyethyl]-beta-D-galactopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；277 K；10 mM sodium phosphate, 137 mM sodium chloride, 2.7 mM potassium chloride, 1.8 mM potassium phosphate	Resolution 2.10 Å R-free 0.251
6W4Z Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzyloxy]-malonyl-beta-D-galactopyranoside Deposited 2020-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–154（153 aa）	Mutation：M54V	SZS methyl 3-O-[3-(benzyloxy)-3-oxopropanoyl]-beta-D-galactopyranoside × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1M sodium citrate dihydrate pH 5.6, 20% PEG 4000, 10% IPA	Resolution 1.59 Å R-free 0.226
6W4Z Galectin-8N terminal domain in complex with Methyl 3-O-[3-O-benzyloxy]-malonyl-beta-D-galactopyranoside Deposited 2020-03-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–154（153 aa）	Mutation：M54V	SZS methyl 3-O-[3-(benzyloxy)-3-oxopropanoyl]-beta-D-galactopyranoside × 1 EDO 1,2-ETHANEDIOL × 1 PG4 TETRAETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298.15 K；0.1M sodium citrate dihydrate pH 5.6, 20% PEG 4000, 10% IPA	Resolution 1.59 Å R-free 0.226
6Z6Y Galectin-8 N-terminal domain in complex with a sulfatide mimicking a sphingolipid Deposited 2020-05-29	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 5–160（156 aa）	Not recorded	L4L [(2~{R},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S})-2-acetamido-3-oxidanylidene-pent-4-enoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl] hydrogen sulfate × 1 ACT ACETATE ION × 6 PGE TRIETHYLENE GLYCOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7.6；298 K；0.1 M Na-HEPES, pH 7.6, 10% PEG 4000 and 20% Isopropanol	Resolution 1.34 Å R-free 0.194
7AEN Galectin-8 N-terminal carbohydrate recognition domain in complex with methyl 3-O-((7-carboxy)quinolin-2-yl)-methoxy)-beta-D-galactopyranoside Deposited 2020-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–156（150 aa）	Not recorded	R8B methyl 3-O-((7-carboxy) quinolin-2-yl)-methyl)-beta-D-galactopyranoside × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；293.5 K；buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).	Resolution 1.60 Å R-free 0.212
7AEN Galectin-8 N-terminal carbohydrate recognition domain in complex with methyl 3-O-((7-carboxy)quinolin-2-yl)-methoxy)-beta-D-galactopyranoside Deposited 2020-09-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 7–156（150 aa）	Not recorded	R8B methyl 3-O-((7-carboxy) quinolin-2-yl)-methyl)-beta-D-galactopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；293.5 K；buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).	Resolution 1.60 Å R-free 0.212
7ALS Alpha and beta Lactose isomer structure of Galectin 8, N-terminal domain Deposited 2020-10-07	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 4–158（155 aa） Chain B 4–158（155 aa）	Not recorded	CL CHLORIDE ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293.5 K；24% (w/v) PEG 2000 MME	Resolution 1.35 Å R-free 0.199
7P11 Galectin-8 N-terminal carbohydrate recognition domain in complex with quinoline D-galactal ligand Deposited 2021-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 7–156（150 aa）	Not recorded	5KM 2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]quinoline-7-carboxylic acid × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；293.5 K；Buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).	Resolution 2.10 Å R-free 0.263
7P11 Galectin-8 N-terminal carbohydrate recognition domain in complex with quinoline D-galactal ligand Deposited 2021-07-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 6–156（151 aa）	Not recorded	5KM 2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]quinoline-7-carboxylic acid × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；293.5 K；Buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).	Resolution 2.10 Å R-free 0.263
7P1M Galectin-8 N-terminal carbohydrate recognition domain in complex with benzimidazole D-galactal ligand Deposited 2021-07-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 6–156（151 aa） Chain B 6–156（151 aa）	Not recorded	4IU 2-[[(2R,3R,4R)-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2H-pyran-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions LIQUID DIFFUSION；pH 8；293.5 K；Buffer (10mM Tris/HCl pH 8.0, 150 mM NaCl, 10 mm lactose and 1 mM TCEP) mixed with reservoir 25% (w/v) PEG 2000 monomethylethyer (MME), a cryo solution (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 10 mM lactose, 25% (w/v) PEG 2000 MME, 20% ethylene glycol (EG) and 1 mM TCEP) and flash-frozen in liquid nitrogen. A co-crystal with lactose, grown from a seeded drop with 24% (w/v) PEG 2000 MME in the reservoir, was used to soak in compound 1 by transferring crystals in three steps to different soaking drops. First to a 2 ul drop with glycerol ( 20% (v/v) glycerol, 25% (w/v PEG 2000 MME, 10 mM Tris/HCl pH 8.0, 50 mM NaCl and 1 mM TCEP) and secondly to a 2 ul drop with 10 mM compound 1 (10 mM Tris/HCl pH 8.0, 50 mM NaCl, 5 mM compound 1, 25% (w/v) PEG 2000 MME and 1 mM TCEP) and thirdly to a second drop with 5 mM compound 1 (same composition as before).	Resolution 1.52 Å R-free 0.207
8HL9 Crystal structure of Galectin-8 C-CRD with part of linker Deposited 2022-11-29	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 171–317（147 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；0.1M Hepes pH 7.0, 0.2M MgCl2, 30% (W/V) PEG 3350	Resolution 1.60 Å R-free 0.251
9FXZ Galectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand Deposited 2024-07-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–317（317 aa）	Not recorded	V19 4-(4-bromophenyl)-2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]phthalazin-1-one × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.5 K；A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, was used to soak the compound by transferring crystals in three steps to soaking drops. These were 2 uL drops with a soaking solution of 20% ethylene glycol, 25% PEG 2000 MME, 10 mM Tris pH 8, 1 mM TCEP, 50 mM NaCl, and 2 mM compound 10. The incubation times in the first two drops were about 10 min and in the third drop about 24 h. Then the crystals were transferred to a cryo solution with the same constituents and flash-frozen in liquid nitrogen.	Resolution 1.30 Å R-free 0.200
9FXZ Galectin-8 N-terminal carbohydrate recognition domain in complex with 4-(bromophenyl)phthalazinone D-galactal ligand Deposited 2024-07-02	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–317（317 aa）	Not recorded	V19 4-(4-bromophenyl)-2-[[(2~{R},3~{R},4~{R})-2-(hydroxymethyl)-3-oxidanyl-3,4-dihydro-2~{H}-pyran-4-yl]oxymethyl]phthalazin-1-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293.5 K；A co-crystal with lactose, grown from 12 mg/ml galectin-8N in 10 mM lactose, 10 mM Tris/HCl pH 8.0, 1 mM TCEP and 150 mM sodium chloride mixed with 25% (w/v) PEG 2000 MME) in a hanging drop, was used to soak the compound by transferring crystals in three steps to soaking drops. These were 2 uL drops with a soaking solution of 20% ethylene glycol, 25% PEG 2000 MME, 10 mM Tris pH 8, 1 mM TCEP, 50 mM NaCl, and 2 mM compound 10. The incubation times in the first two drops were about 10 min and in the third drop about 24 h. Then the crystals were transferred to a cryo solution with the same constituents and flash-frozen in liquid nitrogen.	Resolution 1.30 Å R-free 0.200
9FYJ N-terminal domain of human galectin-8 in complex with an alpha-galactoside ligand Deposited 2024-07-03	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 4–156（153 aa） Chain B 4–156（153 aa）	Not recorded	A1IHE 2-[[(2~{R},3~{R},4~{S},5~{S},6~{R})-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-5-oxidanyl-3-prop-2-ynoxy-oxan-4-yl]oxymethyl]-3-methyl-benzimidazole-5-carboxylic acid × 2 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Drops consisted of 2 ul galectin-8N at 13.1 mg/ml in PBS buffer, 1 mM ligand, 5% DMSO mixed with 2 ul of reservoir solution consisting of 35% (w/v) Morpheus precipitant mix 4, 0.16 M Morpheus alcohol mix, 61 mM MES, 39 mM imidazole, pH 7.5. Morpheus precipitant mix 4 is made up of 25% (w/v) each of methane pentane diol (MPD), polyethylene glycol (PEG) 1000 and PEG 3350. Morpheus alcohol mix contains 0.2 M each of 1,6-hexanediol, 1-butanol, 1,2-propanediol, 2-propanol, 1,4-butanediol and 1,3-propanediol (1.2 M total).	Resolution 1.08 Å R-free 0.150
9KH4 Crystal structure of Galectin-8 N-CRD with N-acetyllactosamine Deposited 2024-11-09	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 4–153（150 aa）	Not recorded	NA SODIUM ION × 1 RNQ ~{N}-[(2~{R},3~{R},4~{R},5~{S},6~{R})-6-(hydroxymethyl)-5-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,4-bis(oxidanyl)oxan-3-yl]ethanamide × 1 NI NICKEL (II) ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；PEG	Resolution 1.75 Å R-free 0.212

36 other PDB entries and 52 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEG8_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–154； UniProt 1–154 Author chain B； PDBConstruct 1–154； UniProt 1–154 Author chain C； PDBConstruct 1–154； UniProt 1–154 Author chain D； PDBConstruct 1–154； UniProt 1–154

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	3ap4
Deposition date deposition_date	2010-10-11
Structure title title	Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose
Keywords keywords	Beta-Sandwich, Galectin, Carbohydrate/Sugar Binding, Sugar Binding Protein; SUGAR BINDING PROTEIN
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	29.48 Å
Radius of gyration Rg (electron density) rg_electron	28.46 Å
Forward intensity I(0) i0	69682200.00
Molecular weight molecular_weight	67572.0 kDa
Excluded volume excluded_volume	85639 Å³
Envelope volume envelope_volume	109990 Å³
Hydration-shell volume shell_volume	32043 Å³
Envelope diameter envelope_diameter	94.2 Å
Shell Rg shell_rg	35.90 Å
Envelope Rg envelope_rg	27.97 Å
Shape Rg shape_rg	28.43 Å
Total Rg total_rg	29.37 Å
Total atoms total_atoms	4775
Residues n_residues	586
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	90.5 Å
Rg (real space) rg_real	29.34 Å
Rg uncertainty (real space) rg_real_error	0.68 Å
I(0) (real space) i0_real	6.9680e+07
I(0) uncertainty (real space) i0_real_error	1.0390e+06
Rg (reciprocal space) rg_reciprocal	29.40 Å
I(0) (reciprocal space) i0_reciprocal	69690000.0000
Solution quality estimate total_estimate	0.9064
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	43.6 Å
Skewness Skewness skewness	0.069
Kurtosis Kurtosis kurtosis	-0.655
Angular range angular_range	— – 0.2700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	29520000.0000
Real-space data points n_real_points	55
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.936; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.999; Smooth: 0.974

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	Galectin-8
Molecular weight formula_weight	17423.1 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5082

MMLSLNNLQNIIYNPVIPFVGTIPDQLDPGTLIVIRGHVPSDADRFQVDLQNGSSVKPRADVAFHFNPRFKRAGCIVCNTLINEKWGREEITYDTPFKREKSFEIVIMVLKDKFQVAVNGKHTLLYGHRIGPEKIDTLGIYGKVNIHSIGFSFS

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 branched

Description description	beta-D-galactopyranose-(1-4)-alpha-D-glucopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	307

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3ap4a_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3ap4b_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3ap4c_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

Domain ID domain_id	d3ap4d_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.0 — automated matches

CATH v4.4 (4 domains)

Domain ID domain_id	3ap4A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3ap4B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3ap4C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3ap4D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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8. Citations (1)

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Unit-cell length a length_a	41.528 Å
Unit-cell length b length_b	64.888 Å
Unit-cell length c length_c	71.584 Å
Unit-cell angle α angle_alpha	98.41 °
Unit-cell angle β angle_beta	105.49 °
Unit-cell angle γ angle_gamma	108.66 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.330 Å
Low-resolution limit resolution_low	51.330 Å
R factor r_factor	0.1936
R_work r_work	0.1908
R_free r_free	0.2514

fit	/app/data/saxs_computation/ap/3ap4/3ap4.fit
pddf	/app/data/pr_computation/ap/3ap4/3ap4.pr.out
profile	/app/data/saxs_computation/ap/3ap4/3ap4.dat