3zxe

Crystal structure of Human Galectin-7 in complex with a galactose- benzylphosphate inhibitor

Method: X-RAY DIFFRACTION D_max: 68.8 Å Quality: GOOD

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

GALECTIN-7

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	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 4–136	Fragment：RESIDUES 4-136	PGZ METHYL 2-O-[(S)-(BENZYLOXY)(HYDROXY)PHOSPHORYL]-3-DEOXY-3-{[(4-METHYLPHENYL)CARBONYL]AMINO}-1-THIO-BETA-D-GALACTOPYRANOSIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.1M BISTRISPROPANE, 20% PEG3350, pH 8.5	Resolution 1.67 Å R-free 0.236
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 4–136	Fragment：RESIDUES 4-136	PGZ METHYL 2-O-[(S)-(BENZYLOXY)(HYDROXY)PHOSPHORYL]-3-DEOXY-3-{[(4-METHYLPHENYL)CARBONYL]AMINO}-1-THIO-BETA-D-GALACTOPYRANOSIDE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：pH 8.5；0.1M BISTRISPROPANE, 20% PEG3350, pH 8.5	Resolution 1.67 Å R-free 0.236

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 3ZXE	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BKZ CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 Deposited 1998-07-13	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 1–135（135 aa） Chain B 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, AND 8.5% PEG 3350. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, AND 17% PEG 3350., vapor diffusion - hanging drop	Resolution 1.90 Å R-free 0.260
2GAL CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSE Deposited 1998-07-13	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 1–135（135 aa） Chain B 1–135（135 aa）	Not recorded	GAL beta-D-galactopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350 AND 25 MM GALACTOSE. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% PEG 3350 AND 50 MM GALACTOSE., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.245
3GAL CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSAMINE Deposited 1998-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–135（135 aa）	Not recorded	1GN 2-amino-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350 AND 25 MM GALACTOSAMINE. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% PEG 3350 AND 50 MM GALACTOSAMINE., vapor diffusion - hanging drop	Resolution 1.90 Å R-free 0.258
3GAL CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH GALACTOSAMINE Deposited 1998-07-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–135（135 aa）	Not recorded	1GN 2-amino-2-deoxy-beta-D-galactopyranose × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350 AND 25 MM GALACTOSAMINE. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% PEG 3350 AND 50 MM GALACTOSAMINE., vapor diffusion - hanging drop	Resolution 1.90 Å R-free 0.258
3ZXF High resolution structure of Human Galectin-7 Deposited 2011-08-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–136（136 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ACT ACETATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；50MM SODIUM PHOSPHATE, 300 MM NACL, 15% PEG3350, 20MM IMIDAZOLE, pH 8.1	Resolution 1.38 Å R-free 0.226
3ZXF High resolution structure of Human Galectin-7 Deposited 2011-08-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–136（136 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.1；50MM SODIUM PHOSPHATE, 300 MM NACL, 15% PEG3350, 20MM IMIDAZOLE, pH 8.1	Resolution 1.38 Å R-free 0.226
4GAL CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH LACTOSE Deposited 1998-07-13	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 1–135（135 aa） Chain B 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% PEG 3350. GALECTIN-7 CRYSTALS WERE THEN SOAKED WITH 5 MM LACTOSE FOR 2 HRS., vapor diffusion - hanging drop	Resolution 1.95 Å R-free 0.255
4UW3 Human galectin-7 in complex with a galactose based dendron D1. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–136（136 aa）	Not recorded	50G DENDRON-D1 × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.05 M BIS TRIS PROPANE PH7, 17 % PEG 3350	Resolution 1.48 Å R-free 0.198
4UW3 Human galectin-7 in complex with a galactose based dendron D1. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.05 M BIS TRIS PROPANE PH7, 17 % PEG 3350	Resolution 1.48 Å R-free 0.198
4UW4 Human galectin-7 in complex with a galactose based dendron D2-1. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.05 M BIS TRIS PROPANE PH 7, 17% PEG 3350	Resolution 1.77 Å R-free 0.235
4UW4 Human galectin-7 in complex with a galactose based dendron D2-1. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–136（136 aa）	Not recorded	4S0 DENDRON D2-1 × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；289 K；0.05 M BIS TRIS PROPANE PH 7, 17% PEG 3350	Resolution 1.77 Å R-free 0.235
4UW5 Human galectin-7 in complex with a galactose based dendron D2-2. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–136（136 aa）	Not recorded	4S0 DENDRON D2-1 × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350	Resolution 2.04 Å R-free 0.319
4UW5 Human galectin-7 in complex with a galactose based dendron D2-2. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350	Resolution 2.04 Å R-free 0.319
4UW5 Human galectin-7 in complex with a galactose based dendron D2-2. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350	Resolution 2.04 Å R-free 0.319
4UW5 Human galectin-7 in complex with a galactose based dendron D2-2. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350	Resolution 2.04 Å R-free 0.319
4UW5 Human galectin-7 in complex with a galactose based dendron D2-2. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350	Resolution 2.04 Å R-free 0.319
4UW5 Human galectin-7 in complex with a galactose based dendron D2-2. Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain F 1–136（136 aa）	Not recorded	4S0 DENDRON D2-1 × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BIS TRIS PROPANE PH7, 14% PEG 3350	Resolution 2.04 Å R-free 0.319
4UW6 Human galectin-7 in complex with a galactose based dendron D3 Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BISTRIS PROPANE PH7, 17% PEG 3350	Resolution 1.79 Å R-free 0.251
4UW6 Human galectin-7 in complex with a galactose based dendron D3 Deposited 2014-08-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–136（136 aa）	Not recorded	VV7 DENDRON-D3 × 1	X-RAY DIFFRACTION X-ray crystallization conditions 0.05M BISTRIS PROPANE PH7, 17% PEG 3350	Resolution 1.79 Å R-free 0.251
4XBQ Crystal Structure of Human Galectin-7 in Complex with Type 1 N-acetyllactosamine Deposited 2014-12-17	Different construct 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 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Hepes pH 7.5, 0.2M Lithium Sulfate, 0.1M Sodium Acetate, 25% (w/v) PEG 4000, temperature 298K	Resolution 2.23 Å R-free 0.225
4XBQ Crystal Structure of Human Galectin-7 in Complex with Type 1 N-acetyllactosamine Deposited 2014-12-17	Different construct 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 1–136（136 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M Hepes pH 7.5, 0.2M Lithium Sulfate, 0.1M Sodium Acetate, 25% (w/v) PEG 4000, temperature 298K	Resolution 2.23 Å R-free 0.225
4Y26 Complex of human Galectin-7 and Galbeta1-3(6OSO3)GlcNAc Deposited 2015-02-09	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 4–136（133 aa） Chain B 4–136（133 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1M HEPES (pH 7.5), 0.2M Li2SO4, 0.1M NaOAc, 25% (w/v) PEG 4000	Resolution 2.61 Å R-free 0.258
5GAL CRYSTAL STRUCTURE OF HUMAN GALECTIN-7 IN COMPLEX WITH N-ACETYLLACTOSAMINE Deposited 1998-07-14	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 1–135（135 aa） Chain B 1–135（135 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.1；CRYSTALS WERE GROWN USING THE HANGING DROP METHOD FROM DROPS CONTAINING 9 MG/ML PROTEIN AT PH 8.1 IN 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 8.5% PEG 3350. DROPS WERE EQUILIBRATED AGAINST RESERVOIRS CONTAINING 50 MM SODIUM PHOSPHATE BUFFER, 0.3 M SODIUM CHLORIDE, 20 MM IMIDAZOLE, 17% PEG 3350. GALECTIN-7 CRYSTALS WERE THEN SOAKED WITH 50 MM N-ACETYLLACTOSAMINE FOR 3 DAYS., vapor diffusion - hanging drop	Resolution 2.00 Å R-free 0.296
5H9Q Crystal Structure of Human Galectin-7 in Complex with TD139 Deposited 2015-12-29	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 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	TD2 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.22 M Mg Acetate, 21% (w/v) PEG3350	Resolution 1.93 Å R-free 0.238
5H9S Crystal Structure of Human Galectin-7 in Complex with TAZTDG Deposited 2015-12-29	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 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	TGZ (2~{S},3~{R},4~{S},5~{R},6~{R})-2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-6-(hydroxymethyl)oxane-3,4,5-triol × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；298 K；0.22 M MgAcetate, 21% (w/v) PEG 3350	Resolution 1.82 Å R-free 0.227
6VTO Crystal structure of human Galectin-7 in complex with 4-O-beta-D-Galactopyranosyl-D-glucose Deposited 2020-02-13	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 2–136（135 aa） Chain B 2–136（135 aa）	Not recorded	LBL (2~{R},3~{R},4~{R},5~{R})-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,3,5, 6-tetrakis(oxidanyl)hexanal × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295 K；0.1 M Sodium Chloride, 0.1 M Tris pH 8, 20 % PEG3350, 5 % Glycerol	Resolution 1.69 Å R-free 0.215
6VTP Crystal structure of G16C human Galectin-7 mutant Deposited 2020-02-13	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：G16C Mutation：G16C	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M Sodium chloride, 0.1M Tris pH 8, 20 % PEG 3350, 15 % Glycerol	Resolution 2.30 Å R-free 0.261
6VTQ Crystal structure of G16C human Galectin-7 mutant in complex with lactose Deposited 2020-02-13	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：G16C Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：G16C Non-standard monomer：Yes (specific site not provided by mmCIF)	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295.15 K；0.1 M Tris pH 8, 0.1 M Sodium Chloride, 25 % PEG3350, 7.5 mM alpha-lactose	Resolution 1.95 Å R-free 0.244
6VTR Crystal structure of G16S human Galectin-7 mutant Deposited 2020-02-13	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：G16S Mutation：G16S	TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8.0, 20 % PEG 3350, 17.5 % Glycerol	Resolution 2.30 Å R-free 0.256
6VTS Crystal structure of G16S human Galectin-7 mutant in complex with lactose Deposited 2020-02-13	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：G16S Mutation：G16S	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；295.15 K；0.1 M Tris pH 8, 0.1 M NaCl, 16 % PEG 3350, 150 mM alpha-Lactose	Resolution 1.90 Å R-free 0.221
7N4O Crystal structure of R20A human Galectin-7 mutant Deposited 2021-06-04	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R20A Mutation：R20A Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000 , 20% Glycerol	Resolution 2.05 Å R-free 0.252
7N57 Crystal structure of R20A human Galectin-7 mutant in presence of lactose Deposited 2021-06-04	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R20A Mutation：R20A	GOL GLYCEROL × 1 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293.15 K；0.2M Sodium chloride, 0.1M Tris pH 8.0, 20% w/v PEG 6000	Resolution 1.83 Å R-free 0.208
7N6C Crystal structure of R22A human Galectin-7 mutant Deposited 2021-06-08	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R22A Mutation：R22A	GOL GLYCEROL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 EDO 1,2-ETHANEDIOL × 5 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 17.5% Glycerol	Resolution 2.10 Å R-free 0.235
7N8D Crystal structure of R22A human Galectin-7 mutant in presence of Lactose Deposited 2021-06-14	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R22A Mutation：R22A Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 7.5 mM alpha Lactose	Resolution 2.49 Å R-free 0.281
7N8G Crystal structure of R20A-R22A human Galectin-7 mutant Deposited 2021-06-14	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R20A, R22A Mutation：R20A, R22A	EDO 1,2-ETHANEDIOL × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000 ,17.5% Glycerol	Resolution 1.95 Å R-free 0.204
7N96 Crystal structure of D103A human Galectin-7 mutant Deposited 2021-06-16	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：D103A Mutation：D103A	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000 ,15% Glycerol	Resolution 2.38 Å R-free 0.259
7RDG Crystal structure of D103A human Galectin-7 mutant in presence of lactose Deposited 2021-07-09	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 C 2–136（135 aa） Chain D 2–136（135 aa）	Mutation：D103A Mutation：D103A	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；295.15 K；0.1 M Tris pH 7.3, 0.1 M NaCl, 18% P400, 26% PEG 3350	Resolution 3.00 Å R-free 0.268
7RDG Crystal structure of D103A human Galectin-7 mutant in presence of lactose Deposited 2021-07-09	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：D103A Mutation：D103A	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.3；295.15 K；0.1 M Tris pH 7.3, 0.1 M NaCl, 18% P400, 26% PEG 3350	Resolution 3.00 Å R-free 0.268
7TKW Crystal structure of R14A human Galectin-7 mutant Deposited 2022-01-17	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R14A Mutation：R14A	GOL GLYCEROL × 4 PEG DI(HYDROXYETHYL)ETHER × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.2 M Sodium chloride, 0.1 M Tris 8.0, 20 % w/v PEG 6000	Resolution 1.85 Å R-free 0.231
7TKX Crystal structure of R14A human Galectin-7 mutant in presence of 4-O-beta-D-Galactopyranosyl-D-glucose Deposited 2022-01-17	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R14A Mutation：R14A	LBL (2~{R},3~{R},4~{R},5~{R})-4-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]oxy-2,3,5, 6-tetrakis(oxidanyl)hexanal × 2 EDO 1,2-ETHANEDIOL × 4 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 10% Glycerol	Resolution 1.83 Å R-free 0.213
7TKY Crystal structure of D94A human Galectin-7 mutant Deposited 2022-01-17	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：D94A Mutation：D94A	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 15% Glycerol	Resolution 2.53 Å R-free 0.283
7TKZ Crystal structure of D94A human Galectin-7 mutant in presence of lactose Deposited 2022-01-17	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：D94A Non-standard monomer：Yes (specific site not provided by mmCIF) Mutation：D94A Non-standard monomer：Yes (specific site not provided by mmCIF)	EDO 1,2-ETHANEDIOL × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8.0, 20 % PEG 6000, 15% glycerol, 7.5 mM Lactose	Resolution 1.83 Å R-free 0.225
7TRN Crystal structure of R14A-R20A human Galectin-7 mutant Deposited 2022-01-29	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R14A, R20A Mutation：R14A, R20A	GOL GLYCEROL × 3 EDO 1,2-ETHANEDIOL × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 17.5% Glycerol	Resolution 1.95 Å R-free 0.225
7TRN Crystal structure of R14A-R20A human Galectin-7 mutant Deposited 2022-01-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 2–136（135 aa） Chain D 2–136（135 aa）	Mutation：R14A, R20A Mutation：R14A, R20A	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl, 0.1 M Tris pH 8, 20 % PEG 6000, 17.5% Glycerol	Resolution 1.95 Å R-free 0.225
7TRO Crystal structure of R14A-R20A human Galectin-7 mutant in presence of lactose Deposited 2022-01-29	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 2–136（135 aa） Chain B 2–136（135 aa）	Mutation：R14A, R20A Mutation：R14A, R20A	EDO 1,2-ETHANEDIOL × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；295.15 K；0.1 M NaCl,0.1 M Tris pH 8, 20 % PEG 6000, 5% Glycerol, 7.5 mM Lactose	Resolution 1.80 Å R-free 0.221
7XAC Dimeric structure of human galectin-7 in complex with two glycerol Deposited 2022-03-17	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 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG 3350, 0.2M Magnesium chloride, 0.1M Hepes pH7.5	Resolution 1.80 Å R-free 0.253
7XBL Dimeric structure of human galectin-7 in complex with three glycerol Deposited 2022-03-21	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 1–136（136 aa） Chain B 1–136（136 aa）	Not recorded	GOL GLYCEROL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；298 K；0.1M Hepes pH7.5, 12% PEG 3350	Resolution 2.00 Å R-free 0.222

34 other PDB entries and 47 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LEG7_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 4–136 Author chain B； PDBConstruct 1–133； UniProt 4–136

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	3zxe
Deposition date deposition_date	2011-08-10
Structure title title	Crystal structure of Human Galectin-7 in complex with a galactose- benzylphosphate inhibitor
Keywords keywords	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	21.51 Å
Radius of gyration Rg (electron density) rg_electron	20.23 Å
Forward intensity I(0) i0	16754400.00
Molecular weight molecular_weight	30381.0 kDa
Excluded volume excluded_volume	37770 Å³
Envelope volume envelope_volume	44822 Å³
Hydration-shell volume shell_volume	19116 Å³
Envelope diameter envelope_diameter	72.0 Å
Shell Rg shell_rg	26.10 Å
Envelope Rg envelope_rg	20.37 Å
Shape Rg shape_rg	20.20 Å
Total Rg total_rg	21.10 Å
Total atoms total_atoms	2147
Residues n_residues	265
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	68.8 Å
Rg (real space) rg_real	21.51 Å
Rg uncertainty (real space) rg_real_error	0.45 Å
I(0) (real space) i0_real	1.6750e+07
I(0) uncertainty (real space) i0_real_error	2.0480e+05
Rg (reciprocal space) rg_reciprocal	21.51 Å
I(0) (reciprocal space) i0_reciprocal	16750000.0000
Solution quality estimate total_estimate	0.8174
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	24.3 Å
Skewness Skewness skewness	0.328
Kurtosis Kurtosis kurtosis	-0.505
Angular range angular_range	— – 0.3700 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3290000.0000
Real-space data points n_real_points	69
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.984; Smooth: 0.000

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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-7
Molecular weight formula_weight	14764.7 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2606

VPHKSSLPEGIRPGTVLRIRGLVPPNASRFHVNLLCGEEQGSDAALHFNPRLDTSEVVFNSKEQGSWGREERGPGVPFQRGQPFEVLIIASDDGFKAVVGDAQYHHFRHRLPLARVRLVEVGGDVQLDSVRIF

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 non-polymer

Description description	METHYL 2-O-[(S)-(BENZYLOXY)(HYDROXY)PHOSPHORYL]-3-DEOXY-3-{[(4-METHYLPHENYL)CARBONYL]AMINO}-1-THIO-BETA-D-GALACTOPYRANOSIDE
Molecular weight formula_weight	497.5 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	364

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7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3zxea_
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.29.1.3 — Galectin (animal S-lectin)

Domain ID domain_id	d3zxeb_
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.29.1.3 — Galectin (animal S-lectin)

CATH v4.4 (2 domains)

Domain ID domain_id	3zxeA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	3zxeB00
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	35.287 Å
Unit-cell length b length_b	53.459 Å
Unit-cell length c length_c	138.646 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.670 Å
Low-resolution limit resolution_low	69.340 Å
R factor r_factor	0.2059
R_work r_work	0.2049
R_free r_free	0.2363

fit	/app/data/saxs_computation/zx/3zxe/3zxe.fit
pddf	/app/data/pr_computation/zx/3zxe/3zxe.pr.out
profile	/app/data/saxs_computation/zx/3zxe/3zxe.dat