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2yro

Solution structure of the C-terminal Gal-bind lectin protein from Human Galectin-8

Method: SOLUTION NMR Dmax: 55.4 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Galectin-8

Homo sapiens

UniProt O00214

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count Chain A； UniProt 175–316 Fragment：Gal-bind_lectin domain No other associated polymer 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

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 2YRO Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
3AP4 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose Deposited 2010-10-11 Different construct Different oligomeric state Different experimental method 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 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, 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
3AP4 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose Deposited 2010-10-11 Different construct Different oligomeric state Different experimental method 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 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, 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
3AP4 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose Deposited 2010-10-11 Different construct Different oligomeric state Different experimental method 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 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, 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
3AP4 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain in complex with lactose Deposited 2010-10-11 Different construct Different oligomeric state Different experimental method 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 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, 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
3AP5 Crystal structure of the galectin-8 N-terminal carbohydrate recognition domain Deposited 2010-10-11 Different construct Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different oligomeric state Different ligand/ion Different experimental method 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 construct Different ligand/ion Different experimental method 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 construct Different ligand/ion Different experimental method 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 experimental method 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 experimental method 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 experimental method 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 experimental method 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 method 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 method 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 method 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 method 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 ligand/ion Different experimental method 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 experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 method 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 method 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 ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 oligomeric state Different ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 experimental method 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 ligand/ion Different experimental method 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 ligand/ion Different experimental method 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 method 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 ligand/ion Different experimental method 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 55 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 8–149； UniProt 175–316

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 2yro

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2yro
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2yro
Deposition date deposition_date2007-04-02
Structure title titleSolution structure of the C-terminal Gal-bind lectin protein from Human Galectin-8
Keywords keywords;Gal-bind lectin, galectin, sugar binding, Structural Genomics, NPPSFA, National Project on Protein Structural and Functional Analyses, RIKEN Structural Genomics/Proteomics Initiative, RSGI, SUGAR BINDING PROTEIN ;; SUGAR BINDING PROTEIN
Experimental Method methodSOLUTION NMR
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier16.04 Å
Radius of gyration Rg (electron density) rg_electron15.29 Å
Forward intensity I(0) i01605490000.00
Molecular weight molecular_weight340230.0 kDa
Excluded volume excluded_volume425800 ų
Envelope volume envelope_volume50669 ų
Hydration-shell volume shell_volume21653 ų
Envelope diameter envelope_diameter65.1 Å
Shell Rg shell_rg26.15 Å
Envelope Rg envelope_rg19.60 Å
Shape Rg shape_rg15.26 Å
Total Rg total_rg15.56 Å
Total atoms total_atoms47740
Residues n_residues3100
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 dmax55.4 Å
Rg (real space) rg_real15.94 Å
Rg uncertainty (real space) rg_real_error0.38 Å
I(0) (real space) i0_real1.6050e+09
I(0) uncertainty (real space) i0_real_error1.9130e+07
Rg (reciprocal space) rg_reciprocal15.95 Å
I(0) (reciprocal space) i0_reciprocal1605000000.0000
Solution quality estimate total_estimate0.7715
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary20.3 Å
Skewness Skewness skewness0.148
Kurtosis Kurtosis kurtosis-0.209
Angular range angular_range— – 0.4950 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha732400.0000
Real-space data points n_real_points80
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.676; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd2yroa1
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.0 — automated matches
Domain ID domain_idd2yroa2
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2yroa3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id2yroA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
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8. Citations (1)

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9. Files and Curves (10)