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1v6o

Peanut lectin complexed with 10mer peptide (PVRIWSSATG)

Method: X-RAY DIFFRACTION Dmax: 144.7 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Galactose-binding lectin

OrganismNot specified

UniProt P02872

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 24–255 Chain B； UniProt 24–255 Chain C； UniProt 24–255 Chain D； UniProt 24–255 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
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain E； UniProt 24–255 Chain F； UniProt 24–255 Chain G； UniProt 24–255 Chain H； UniProt 24–255 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

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 1V6O 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 oligomeric state 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 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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 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 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 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 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
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 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） 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 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） 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 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） 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 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） 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
2DVF Crystals of peanut lectin grown in the presence of GAL-ALPHA-1,3-GAL-BETA-1,4-GAL Deposited 2006-07-31 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） 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
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
2DVG Crystal structure of peanut lectin GAL-ALPHA-1,6-GLC complex Deposited 2006-07-31 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） 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 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 28 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 1–232； UniProt 24–255 Author chain B； PDBConstruct 1–232； UniProt 24–255 Author chain C； PDBConstruct 1–232； UniProt 24–255 Author chain D； PDBConstruct 1–232； UniProt 24–255 Author chain E； PDBConstruct 1–232； UniProt 24–255 Author chain F； PDBConstruct 1–232； UniProt 24–255 Author chain G； PDBConstruct 1–232； UniProt 24–255 Author chain H； PDBConstruct 1–232； UniProt 24–255

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 1v6o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1v6o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1v6o
Deposition date deposition_date2003-12-02
Structure title titlePeanut lectin complexed with 10mer peptide (PVRIWSSATG)
Keywords keywordsLectin, agglutinin, open quaternary association, monoclinic and peptide, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier51.07 Å
Radius of gyration Rg (electron density) rg_electron50.78 Å
Forward intensity I(0) i0559516000.00
Molecular weight molecular_weight198200.0 kDa
Excluded volume excluded_volume247740 ų
Envelope volume envelope_volume341350 ų
Hydration-shell volume shell_volume54643 ų
Envelope diameter envelope_diameter157.7 Å
Shell Rg shell_rg57.42 Å
Envelope Rg envelope_rg48.96 Å
Shape Rg shape_rg50.76 Å
Total Rg total_rg51.01 Å
Total atoms total_atoms13968
Residues n_residues1856
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 dmax144.7 Å
Rg (real space) rg_real51.18 Å
Rg uncertainty (real space) rg_real_error1.00 Å
I(0) (real space) i0_real5.5950e+08
I(0) uncertainty (real space) i0_real_error9.2940e+06
Rg (reciprocal space) rg_reciprocal50.94 Å
I(0) (reciprocal space) i0_reciprocal559300000.0000
Solution quality estimate total_estimate0.8045
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary42.0 Å
Skewness Skewness skewness0.203
Kurtosis Kurtosis kurtosis-1.020
Angular range angular_range— – 0.1550 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha28960000.0000
Real-space data points n_real_points32
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.865; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.861; Smooth: 0.000
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

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7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1v6oa_
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.29.1.1 — Legume lectins
Domain ID domain_idd1v6ob_
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.29.1.1 — Legume lectins
Domain ID domain_idd1v6oc_
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.29.1.1 — Legume lectins
Domain ID domain_idd1v6od_
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.29.1.1 — Legume lectins
Domain ID domain_idd1v6oe_
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.29.1.1 — Legume lectins
Domain ID domain_idd1v6of_
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.29.1.1 — Legume lectins
Domain ID domain_idd1v6og_
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.29.1.1 — Legume lectins
Domain ID domain_idd1v6oh_
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.29.1.1 — Legume lectins

CATH v4.4 (8 domains)

Domain ID domain_id1v6oA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1v6oB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1v6oC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1v6oD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1v6oE00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1v6oF00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1v6oG00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id1v6oH00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
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8. Citations (2)

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9. Files and Curves (10)