SAXSdb — 2dvf

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

Galactose-binding lectin

OrganismNot specified

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 homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 24–259 Chain B； UniProt 24–259 Chain C； UniProt 24–259 Chain D； UniProt 24–259	Fragment：residues 1-236	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；7.5% PEG 8000, 0.025M Sodium cadodylate, 0.5M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.74 Å R-free 0.263

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 2DVF	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BZW PEANUT LECTIN COMPLEXED WITH C-LACTOSE Deposited 1998-11-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP OF 5 MG/ML PROTEIN IN 0.05 M SODIUM PHOSPHATE BUFFER,PH 7.0, CONTAINING 0.2M SODIUM CHLORIDE, 0.02 % SODIUM AZIDE, 10MM C-LACTOSE AND 12% (W/V) PEG 8000 IN THE SAME BUFFER, vapor diffusion - hanging drop	Resolution 2.70 Å R-free 0.227
1CQ9 PEANUT LECTIN-TRICLINIC FORM Deposited 1999-08-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 1–236（236 aa） Chain B 1–236（236 aa） Chain C 1–236（236 aa） Chain D 1–236（236 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；pH 4.6	Resolution 3.50 Å R-free 0.278
1QF3 PEANUT LECTIN COMPLEXED WITH METHYL-BETA-GALACTOSE Deposited 1999-04-06	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	MBG methyl beta-D-galactopyranoside × 4 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；HANGING DROP OF 5 MG/ML PROTEIN IN 0.05 M SODIUM PHOSPHATE BUFFER,PH 7.0, CONTAINING 0.2M SODIUM CHLORIDE, 0.02 % SODIUM AZIDE, 1.5-10MM METHYL-BETA- GALACTOSE AND 12% (W/V) PEG 8000 IN THE SAME BUFFER, VAPOR DIFFUSION, HANGING DROP	Resolution 2.80 Å R-free 0.247
1RIR Crystal structure of meso-tetrasulphonatophenylporphyrin in complex with Peanut lectin. Deposited 2003-11-17	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 SFP 5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE × 11	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；ammonium sulphate, Sodium Chloride, Phosphate buffer, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 2.90 Å R-free 0.282
1RIT Crystal structure of Peanut lectin in complex with meso-tetrasulphonatophenylporphyrin and lactose Deposited 2003-11-17	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	SFP 5,10,15,20-TETRAKIS(4-SULPFONATOPHENYL)-21H,23H-PORPHINE × 11 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.2；298 K；Ammonium sulphate, Sodium Chloride, Phosphate buffe, pH 7.2, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.85 Å R-free 0.260
1V6I Peanut lectin-lactose complex in acidic pH Deposited 2003-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop method；pH 4.6；293 K；PEG 8000, 0.2M calcium acetate, 0.1M cacodylate pH 6.5, pH 4.6, hanging drop method, temperature 293K	Resolution 2.15 Å R-free 0.218
1V6J peanut lectin-lactose complex crystallized in orthorhombic form at acidic pH Deposited 2003-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；293 K；PEG 8000, 0.05M sodium acetate buffer, 0.2M NaCl, 0.05% Sodium azide, pH 4.6, hanging drop method, temperature 293K	Resolution 2.90 Å R-free 0.220
1V6K Peanut lectin-lactose complex in the presence of peptide(IWSSAGNVA) Deposited 2003-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions Hanging drop method；pH 4.6；293 K；PEG 8000, 0.2M calcium acetate, 0.1M cacodylate pH 6.5, pH 4.6, Hanging drop method, temperature 293K	Resolution 2.40 Å R-free 0.219
1V6L Peanut lectin-lactose complex in the presence of 9mer peptide (PVIWSSATG) Deposited 2003-12-01	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions Hanging drop method；pH 4.6；293 K；PEG 8000, 0.2M calcium acetate, 0.1M cacodylate pH 6.5, pH 4.6, Hanging drop method, temperature 293K	Resolution 2.50 Å R-free 0.219
1V6M Peanut Lectin with 9mer peptide (IWSSAGNVA) Deposited 2003-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop method；pH 4.6；293 K；30% PEG8000, 0.2M Ammonium sulfate and 0.1M cacodylate, pH 4.6, hanging drop method, temperature 293K	Resolution 2.70 Å R-free 0.264
1V6M Peanut Lectin with 9mer peptide (IWSSAGNVA) Deposited 2003-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 24–255（232 aa） Chain F 24–255（232 aa） Chain G 24–255（232 aa） Chain H 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop method；pH 4.6；293 K；30% PEG8000, 0.2M Ammonium sulfate and 0.1M cacodylate, pH 4.6, hanging drop method, temperature 293K	Resolution 2.70 Å R-free 0.264
1V6N Peanut lectin with 9mer peptide (PVIWSSATG) Deposited 2003-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop method；pH 4.6；293 K；30% PEG8000, 0.2M Ammonium sulfate and 0.1M cacodylate, pH 4.6, hanging drop method, temperature 293K	Resolution 3.50 Å R-free 0.292
1V6N Peanut lectin with 9mer peptide (PVIWSSATG) Deposited 2003-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 24–255（232 aa） Chain F 24–255（232 aa） Chain G 24–255（232 aa） Chain H 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop method；pH 4.6；293 K；30% PEG8000, 0.2M Ammonium sulfate and 0.1M cacodylate, pH 4.6, hanging drop method, temperature 293K	Resolution 3.50 Å R-free 0.292
1V6O Peanut lectin complexed with 10mer peptide (PVRIWSSATG) Deposited 2003-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–255（232 aa） Chain B 24–255（232 aa） Chain C 24–255（232 aa） Chain D 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop method；pH 4.6；293 K；30% PEG 8000, 0.2M Ammonium sulfate and 0.1M cacodylate pH6.5, pH 4.6, hanging drop method, temperature 293K	Resolution 3.00 Å R-free 0.239
1V6O Peanut lectin complexed with 10mer peptide (PVRIWSSATG) Deposited 2003-12-02	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain E 24–255（232 aa） Chain F 24–255（232 aa） Chain G 24–255（232 aa） Chain H 24–255（232 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions hanging drop method；pH 4.6；293 K；30% PEG 8000, 0.2M Ammonium sulfate and 0.1M cacodylate pH6.5, pH 4.6, hanging drop method, temperature 293K	Resolution 3.00 Å R-free 0.239
2DH1 Crystal structure of peanut lectin lactose-azobenzene-4,4'-dicarboxylic acid-lactose complex Deposited 2006-03-17	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 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；12% PEG 8000, 0.05M sodium phosphate, 0.2M sodium cholride, 0.02% sodium azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 7.65 Å R-free 0.377
2DH1 Crystal structure of peanut lectin lactose-azobenzene-4,4'-dicarboxylic acid-lactose complex Deposited 2006-03-17	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 B 24–259（236 aa） Chain C 24–259（236 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；12% PEG 8000, 0.05M sodium phosphate, 0.2M sodium cholride, 0.02% sodium azide, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 7.65 Å R-free 0.377
2DV9 Crystal structure of peanut lectin GAL-BETA-1,3-GAL complex Deposited 2006-07-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Fragment：residues 1-236 Chain B 24–259（236 aa） Fragment：residues 1-236 Chain C 24–259（236 aa） Fragment：residues 1-236 Chain D 24–259（236 aa） Fragment：residues 1-236	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；7.5% PEG 8000, 0.025M Sodium cadodylate, 0.5M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.48 Å R-free 0.257
2DVA Crystal structure of peanut lectin GAL-BETA-1,3-GALNAC-ALPHA-O-ME (Methyl-T-antigen) complex Deposited 2006-07-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Fragment：residues 1-236 Chain B 24–259（236 aa） Fragment：residues 1-236 Chain C 24–259（236 aa） Fragment：residues 1-236 Chain D 24–259（236 aa） Fragment：residues 1-236	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；7.5% PEG 8000, 0.025M Sodium cadodylate, 0.5M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.20 Å R-free 0.250
2DVB Crystal structure of peanut lectin GAl-beta-1,6-GalNAc complex Deposited 2006-07-30	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Fragment：residues 1-236 Chain B 24–259（236 aa） Fragment：residues 1-236 Chain C 24–259（236 aa） Fragment：residues 1-236 Chain D 24–259（236 aa） Fragment：residues 1-236	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 SO4 SULFATE ION × 4 GAL beta-D-galactopyranose × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；7.5% PEG 8000, 0.025M Sodium cadodylate, 0.5M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.25 Å R-free 0.266
2DVD Crystal structure of peanut lectin GAL-ALPHA-1,3-GAL complex Deposited 2006-07-31	Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Fragment：residues 1-236 Chain B 24–259（236 aa） Fragment：residues 1-236 Chain C 24–259（236 aa） Fragment：residues 1-236 Chain D 24–259（236 aa） Fragment：residues 1-236	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 SO4 SULFATE ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å R-free 0.232
2DVG Crystal structure of peanut lectin GAL-ALPHA-1,6-GLC complex Deposited 2006-07-31	Different oligomeric state Different ligand/ion Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Fragment：residues 1-236 Chain B 24–259（236 aa） Fragment：residues 1-236 Chain C 24–259（236 aa） Fragment：residues 1-236 Chain D 24–259（236 aa） Fragment：residues 1-236	Not recorded	GLA alpha-D-galactopyranose × 3 CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4 SO4 SULFATE ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；288 K；7.5% PEG 8000, 0.025M Sodium cadodylate, 0.5M ammonium sulfate, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.78 Å R-free 0.274
2PEL PEANUT LECTIN Deposited 1995-08-23	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	CA CALCIUM ION × 4 MN MANGANESE (II) ION × 4	X-RAY DIFFRACTION mmCIF provides none of the parsed conditions	Resolution 2.25 Å
6V95 Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L-tartaramidoyl derivative (diNGT) Deposited 2019-12-13	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	QSG (2R,3R)-N-[(1-{(3S,3aR,6S,6aR)-6-[4-({[(2R,3R)-2,3-dihydroxy-4-oxo-4-{[(2R,3R,4R,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]amino}butanoyl]amino}methyl)-1H-1,2,3-triazol-1-yl]hexahydrofuro[3,2-b]furan-3-yl}-1H-1,2,3-triazol-4-yl)methyl]-2,3-dihydroxy-N'-[(2R,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]butanediamide (non-preferred name) × 4 MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% (w/v) PEG 8000, 0.1M sodium citrate, 0.1M ammonium sulfate	Resolution 1.78 Å R-free 0.243
6VAV Peanut lectin complexed with divalent N-beta-D-galactopyranosyl-L-succinamoyl derivative (diNGS) Deposited 2019-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	QTY N-[[1-[(3S,3aR,6S,6aR)-6-[4-[[[4-[[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]amino]-4-oxidanylidene-butanoyl]amino]methyl]-1,2,3-triazol-1-yl]-2,3,3a,5,6,6a-hexahydrofuro[3,2-b]furan-3-yl]-1,2,3-triazol-4-yl]methyl]-N'-[(2R,3R,4S,5R,6R)-6-(hydroxymethyl)-3,4,5-tris(oxidanyl)oxan-2-yl]butanediamide × 4 MN MANGANESE (II) ION × 3 CA CALCIUM ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% (w/v) PEG 8000, 0.1M sodium citrate, 0.1M ammonium sulfate	Resolution 1.85 Å R-free 0.225
6VAW Peanut lectin complexed with N-beta-D-galactopyranosyl-L-succinamoyl derivative (NGS) Deposited 2019-12-18	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	S3W N-[(2R,3R,4S,5R,6S)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]-N'-[(1-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-methoxytetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]butanediamide × 4 MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% (w/v) PEG 8000, 0.1M sodium citrate, 0.05M ammonium sulfate	Resolution 1.75 Å R-free 0.232
6VC3 Peanut lectin complexed with S-beta-D-thiogalactopyranosyl 6-deoxy-6-S-propynyl-beta-D-glucopyranoside (STG) Deposited 2019-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	QWJ 6-S-(prop-2-yn-1-yl)-6-thio-beta-D-glucopyranosyl 1-thio-beta-D-galactopyranoside × 3 MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% (w/v) PEG 8000, 0.1 sodium citrate, 0.125M ammonium sulfate	Resolution 1.95 Å R-free 0.283
6VC4 Peanut lectin complexed with S-beta-D-Thiogalactopyranosyl beta-D-glucopyranoside derivative (STGD) Deposited 2019-12-20	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	QWG (2R,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-({[(1-{[(2R,3S,4S,5R,6S)-3,4,5-trihydroxy-6-methoxytetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]sulfanyl}methyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-3,4,5-triol (non-preferred name) × 4 MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% (w/v) PEG 8000, 0.1 sodium citrate, 0.125M ammonium sulfate	Resolution 1.90 Å R-free 0.244
6VGF Peanut lectin complexed with divalent S-beta-D-thiogalactopyranosyl beta-D-glucopyranoside derivative (diSTGD) Deposited 2020-01-08	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric	Chain A 24–259（236 aa） Chain B 24–259（236 aa） Chain C 24–259（236 aa） Chain D 24–259（236 aa）	Not recorded	WA3 (2S,3R,4S,5R,6S)-2-(hydroxymethyl)-6-{[(2S,3R,4S,5S,6S)-3,4,5-trihydroxy-6-({[(1-{[(2R,3S,4S,5R,6R)-3,4,5-trihydroxy-6-{[(2R,3R,4S,5S,6R)-3,4,5-trihydroxy-6-({4-[({[(2S,3S,4S,5R,6S)-3,4,5-trihydroxy-6-{[(2S,3R,4S,5R,6R)-3,4,5-trihydroxy-6-(hydroxymethyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-2-yl]methyl}sulfanyl)methyl]-1H-1,2,3-triazol-1-yl}methyl)tetrahydro-2H-pyran-2-yl]oxy}tetrahydro-2H-pyran-2-yl]methyl}-1H-1,2,3-triazol-4-yl)methyl]sulfanyl}methyl)tetrahydro-2H-pyran-2-yl]sulfanyl}tetrahydro-2H-pyran-3,4,5-triol × 4 MN MANGANESE (II) ION × 4 CA CALCIUM ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；294 K；15% (w/v) PEG 8000, 0.1M sodium citrate, 0.125M ammonium sulfate	Resolution 1.83 Å R-free 0.243

25 other PDB entries and 29 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	LECG_ARAHY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–236； UniProt 24–259 Author chain B； PDBConstruct 1–236； UniProt 24–259 Author chain C； PDBConstruct 1–236； UniProt 24–259 Author chain D； PDBConstruct 1–236； UniProt 24–259

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2dvf
Deposition date deposition_date	2006-07-31
Structure title title	Crystals of peanut lectin grown in the presence of GAL-ALPHA-1,3-GAL-BETA-1,4-GAL
Keywords keywords	LEGUME LECTIN, AGGLUTININ, OPEN QUATERNARY STRUCTURE, CARBOHYDRATE SPECIFICITY, 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	30.16 Å
Radius of gyration Rg (electron density) rg_electron	28.91 Å
Forward intensity I(0) i0	158008000.00
Molecular weight molecular_weight	99418.0 kDa
Excluded volume excluded_volume	124040 Å³
Envelope volume envelope_volume	145750 Å³
Hydration-shell volume shell_volume	40918 Å³
Envelope diameter envelope_diameter	92.5 Å
Shell Rg shell_rg	37.10 Å
Envelope Rg envelope_rg	28.67 Å
Shape Rg shape_rg	28.87 Å
Total Rg total_rg	29.73 Å
Total atoms total_atoms	7000
Residues n_residues	928
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	91.2 Å
Rg (real space) rg_real	29.97 Å
Rg uncertainty (real space) rg_real_error	0.57 Å
I(0) (real space) i0_real	1.5800e+08
I(0) uncertainty (real space) i0_real_error	2.3590e+06
Rg (reciprocal space) rg_reciprocal	30.06 Å
I(0) (reciprocal space) i0_reciprocal	158000000.0000
Solution quality estimate total_estimate	0.9075
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	89.5 Å
Skewness Skewness skewness	0.072
Kurtosis Kurtosis kurtosis	-0.588
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	22530000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.958; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.931

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Galactose-binding lectin
Molecular weight formula_weight	25209.0 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7448

AETVSFNFNSFSEGNPAINFQGDVTVLSNGNIQLTNLNKVNSVGRVLYAMPVRIWSSATGNVASFLTSFSFEMKDIKDYDPADGIIFFIAPEDTQIPAGSIGGGTLGVSDTKGAGHFVGVEFDTYSNSEYNDPPTDHVGIDVNSVDSVKTVPWNSVSGAVVKVTVIYDSSTKTLSVAVTNDNGDITTIAQVVDLKAKLPERVKFGFSASGSLGGRQIHLIRSWSFTSTLITTTRRS

Entity 2 Entity 2 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	448

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2dvfa_
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.29.1.1 — Legume lectins

Domain ID domain_id	d2dvfb_
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.29.1.1 — Legume lectins

Domain ID domain_id	d2dvfc_
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.29.1.1 — Legume lectins

Domain ID domain_id	d2dvfd_
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.29.1.1 — Legume lectins

CATH v4.4 (4 domains)

Domain ID domain_id	2dvfA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2dvfB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2dvfC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2dvfD00
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 (6)

;Structural studies on peanut lectin complexed with disaccharides involving different linkages: further insights into the structure and interactions of the lectin ;

ACTA CRYSTALLOGR.,SECT.D (2006)

PMID: 17057347 · DOI: 10.1107/S0907444906035712 PRIMARY

Multivalency in Lectins. A Crystallographic Modellin and Light-Scattering Study Involving Peanut Lectin and a Bivalent Ligand

Curr.Sci. (2006)

Structural plasticity of peanut lectin: an X-ray analysis involving variation in pH, ligand binding and crystal structure

ACTA CRYSTALLOGR.,SECT.D (2004)

PMID: 14747696 · DOI: 10.1107/S090744490302849X

The Specificity of Peanut Agglutinin for Thomsen-Friedenreich Antigen is Mediated by Water-Bridges

Curr.Sci. (1997)

;Conformation, protein-carbohydrate interactions and a novel subunit association in the refined structure of peanut lectin-lactose complex ;

J.Mol.Biol. (1996)

PMID: 8656429 · DOI: 10.1006/jmbi.1996.0319

Crystal structure of peanut lectin, a protein with an unusual quaternary structure

Proc.Natl.Acad.Sci.USA (1994)

PMID: 8278370 · DOI: 10.1073/pnas.91.1.227

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Unit-cell length a length_a	125.810 Å
Unit-cell length b length_b	124.060 Å
Unit-cell length c length_c	75.400 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	16

Space group space_group	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.740 Å
Low-resolution limit resolution_low	19.940 Å
R factor r_factor	0.2000
R_work r_work	0.2000
R_free r_free	0.2630

fit	/app/data/saxs_computation/dv/2dvf/2dvf.fit
pddf	/app/data/pr_computation/dv/2dvf/2dvf.pr.out
profile	/app/data/saxs_computation/dv/2dvf/2dvf.dat

Crystals of peanut lectin grown in the presence of GAL-ALPHA-1,3-GAL-BETA-1,4-GAL

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

Galactose-binding lectin

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction