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1onk

Mistletoe lectin I from viscum album

Method: X-RAY DIFFRACTION Dmax: 83.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Beta-galactoside specific lectin I A chain

OrganismNot specified

UniProt P81446

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain A； UniProt 1–254 Not recorded Galactose specific lectin I B chain × 2 （P81830） PO4 PHOSPHATE ION × 2 AZI AZIDE ION × 18 GOL GLYCEROL × 16 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；40% saturated ammonium sulphate, 30% glycerol in 0.1M, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.223
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain A； UniProt 1–254 Not recorded Galactose specific lectin I B chain × 1 （P81830） PO4 PHOSPHATE ION × 1 AZI AZIDE ION × 9 GOL GLYCEROL × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；40% saturated ammonium sulphate, 30% glycerol in 0.1M, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.223

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 1ONK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1M2T Mistletoe Lectin I from Viscum album in Complex with Adenine Monophosphate. Crystal Structure at 1.9 A Resolution Deposited 2002-06-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 1–254（254 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 FUC alpha-L-fucopyranose × 2 ADE ADENINE × 1 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions vapor diffusion under microgravity；pH 2.5；293 K；ammonium sulphate, pH 2.5, vapor diffusion under microgravity at 293K
Resolution 1.89 Å R-free 0.240
1PUM Mistletoe lectin I in complex with galactose Deposited 2003-06-25 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 34–282（249 aa）
Chain B 302–564（263 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 16 GAL beta-D-galactopyranose × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；ammonium sulphate, glycin-HCL, galactose, dioxan, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.30 Å R-free 0.246
1SZ6 MISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A RESOLUTION Deposited 2004-04-04 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 4 PDB declaration: tetrameric
Chain A 34–282（249 aa）
Chain B 302–564（263 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 SO4 SULFATE ION × 2 AZI AZIDE ION × 6 CL CHLORIDE ION × 4 GOL GLYCEROL × 30 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；40% SATURATED AMMONIUM SULPHATE, 30% GLYCEROL IN 0.1M, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.05 Å R-free 0.253
2R9K Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide Deposited 2007-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Other combination Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 302–564（263 aa） Fragment：Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 4 GOL GLYCEROL × 4 CL CHLORIDE ION × 1 SGI 3-(4-hydroxyphenyl)propanamide × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.267
2R9K Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide Deposited 2007-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 302–564（263 aa） Fragment：Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 SO4 SULFATE ION × 8 GOL GLYCEROL × 8 CL CHLORIDE ION × 2 SGI 3-(4-hydroxyphenyl)propanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.267
2R9K Crystal Structure of Misteltoe Lectin I in Complex with Phloretamide Deposited 2007-09-13 Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 3 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric
Chain B 302–564（263 aa） Fragment：Beta-galactoside-specific lectin 1 chain B, UNP residues 302-564
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8 SO4 SULFATE ION × 8 GOL GLYCEROL × 8 CL CHLORIDE ION × 2 SGI 3-(4-hydroxyphenyl)propanamide × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Resolution 2.70 Å R-free 0.267
2RG9 Crystal structure of viscum album mistletoe lectin I in native state at 1.95 A resolution, comparison of structure active site conformation in ricin and in viscumin Deposited 2007-10-03 Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric
Chain A 34–282（249 aa）
Chain B 302–564（263 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 SO4 SULFATE ION × 1 AZI AZIDE ION × 3 CL CHLORIDE ION × 2 GOL GLYCEROL × 15 X-RAY DIFFRACTION mmCIF provides none of the parsed conditions Resolution 1.95 Å R-free 0.239
3D7W Mistletoe Lectin I in Complex with Zeatin Deposited 2008-05-22 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 34–287（254 aa） Fragment：Beta-galactoside-specific lectin 1 chain A isoform 1
Chain B 302–564（263 aa） Fragment：Beta-galactoside-specific lectin 1 chain B
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 SO4 SULFATE ION × 2 GOL GLYCEROL × 4 ZEA (2E)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol × 1 ZEZ (2Z)-2-methyl-4-(9H-purin-6-ylamino)but-2-en-1-ol × 1 X-RAY DIFFRACTION
X-ray crystallization conditions LIQUID DIFFUSION；pH 2.5；293 K；counter diffusion under microgravity conditions during JAXA-GCF-flight number 6, pH 2.5, LIQUID DIFFUSION, temperature 293K
Resolution 2.49 Å R-free 0.224
3O5W Binding of kinetin in the active site of mistletoe lectin I Deposited 2010-07-28 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 34–287（254 aa）
Chain B 302–564（263 aa）
Not recorded SO4 SULFATE ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 GOL GLYCEROL × 8 H35 N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE × 1 X-RAY DIFFRACTION
X-ray crystallization conditions COUNTER-DIFFUSION；pH 2.5；293 K；1.0M ammonium sulphate, 0.2M glycine/HCl, pH 2.5, counter diffusion, temperature 293K
Resolution 2.70 Å R-free 0.226
4JKX Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution. Deposited 2013-03-12 Different construct Different mutation/modification 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 34–282（249 aa）
Chain B 302–564（263 aa）
Not recorded SO4 SULFATE ION × 10 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 GOL GLYCEROL × 20 H35 N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE × 2 EDO 1,2-ETHANEDIOL × 12 DIO 1,4-DIETHYLENE DIOXIDE × 2 CL CHLORIDE ION × 4 AZI AZIDE ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；1.0M ammonium sulphate, 0.2M glycine/HCl, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.35 Å R-free 0.248
4JKX Crystal structure Mistletoe Lectin I from Viscum album in complex with kinetin at 2.35 A resolution. Deposited 2013-03-12 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 34–282（249 aa）
Chain B 302–564（263 aa）
Not recorded SO4 SULFATE ION × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 GOL GLYCEROL × 10 H35 N-(FURAN-2-YLMETHYL)-7H-PURIN-6-AMINE × 1 EDO 1,2-ETHANEDIOL × 6 DIO 1,4-DIETHYLENE DIOXIDE × 1 CL CHLORIDE ION × 2 AZI AZIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；1.0M ammonium sulphate, 0.2M glycine/HCl, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K
Resolution 2.35 Å R-free 0.248
9KX8 Mistletoe Lectin I from Viscum album complexed with epimer form of lactose Deposited 2024-12-06 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 34–280（247 aa）
Chain B 302–564（263 aa）
Not recorded GOL GLYCEROL × 5 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 SO4 SULFATE ION × 3 GLY GLYCINE × 1 CL CHLORIDE ION × 2 NA SODIUM ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；0.2M Glycin, 30% AmSO4, 4% Dioxane
Resolution 2.28 Å R-free 0.231

9 other PDB entries and 12 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ML1_VISAL
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–254； UniProt 1–254

Galactose specific lectin I B chain

OrganismNot specified

UniProt P81830

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count Chain B； UniProt 1–264 Not recorded Beta-galactoside specific lectin I A chain × 2 （P81446） PO4 PHOSPHATE ION × 2 AZI AZIDE ION × 18 GOL GLYCEROL × 16 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；40% saturated ammonium sulphate, 30% glycerol in 0.1M, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.223
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count Chain B； UniProt 1–264 Not recorded Beta-galactoside specific lectin I A chain × 1 （P81446） PO4 PHOSPHATE ION × 1 AZI AZIDE ION × 9 GOL GLYCEROL × 8 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 2.5；293 K；40% saturated ammonium sulphate, 30% glycerol in 0.1M, pH 2.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K Resolution 2.10 Å R-free 0.223

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 1ONK Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
1CE7 MISTLETOE LECTIN I FROM VISCUM ALBUM Deposited 1999-03-18 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–264（260 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.70 Å R-free 0.319
1M2T Mistletoe Lectin I from Viscum album in Complex with Adenine Monophosphate. Crystal Structure at 1.9 A Resolution Deposited 2002-06-25 Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 1–264（264 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 6 FUC alpha-L-fucopyranose × 2 ADE ADENINE × 1 GOL GLYCEROL × 8 X-RAY DIFFRACTION
X-ray crystallization conditions vapor diffusion under microgravity；pH 2.5；293 K；ammonium sulphate, pH 2.5, vapor diffusion under microgravity at 293K
Resolution 1.89 Å R-free 0.240
2MLL MISTLETOE LECTIN I FROM VISCUM ALBUM Deposited 1999-03-16 Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 5–264（260 aa）
Not recorded NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 3 X-RAY DIFFRACTION
X-ray crystallization conditions pH 4.5；pH 4.5
Resolution 2.70 Å R-free 0.319

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name MLB1_VISAL
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–263； UniProt 1–264

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 1onk

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id1onk
Deposition date deposition_date2003-02-28
Structure title titleMistletoe lectin I from viscum album
Keywords keywordsRIBOSOME-INACTIVATING PROTEIN TYPE II, hydrolase-sugar binding protein COMPLEX; hydrolase/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_guinier26.26 Å
Radius of gyration Rg (electron density) rg_electron25.22 Å
Forward intensity I(0) i061066200.00
Molecular weight molecular_weight58468.0 kDa
Excluded volume excluded_volume72163 ų
Envelope volume envelope_volume84695 ų
Hydration-shell volume shell_volume28491 ų
Envelope diameter envelope_diameter87.2 Å
Shell Rg shell_rg32.13 Å
Envelope Rg envelope_rg25.30 Å
Shape Rg shape_rg25.21 Å
Total Rg total_rg25.93 Å
Total atoms total_atoms4112
Residues n_residues512
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 dmax83.9 Å
Rg (real space) rg_real26.28 Å
Rg uncertainty (real space) rg_real_error0.64 Å
I(0) (real space) i0_real6.1070e+07
I(0) uncertainty (real space) i0_real_error1.0160e+06
Rg (reciprocal space) rg_reciprocal26.27 Å
I(0) (reciprocal space) i0_reciprocal61070000.0000
Solution quality estimate total_estimate0.8962
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary28.0 Å
Skewness Skewness skewness0.377
Kurtosis Kurtosis kurtosis-0.386
Angular range angular_range— – 0.3000 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha9428000.0000
Real-space data points n_real_points61
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.905; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.946
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_idd1onka_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamilyd.165.1 — Ribosome inactivating proteins (RIP)
Family Family familyd.165.1.1 — Plant cytotoxins
Domain ID domain_idd1onkb1
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.2 — Ricin B-like lectins
Family Family familyb.42.2.1 — Ricin B-like
Domain ID domain_idd1onkb2
Class classb — All beta proteins
Fold Fold foldb.42 — beta-Trefoil
Superfamily Superfamily superfamilyb.42.2 — Ricin B-like lectins
Family Family familyb.42.2.1 — Ricin B-like

CATH v4.4 (4 domains)

Domain ID domain_id1onkA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily10 — Ricin (A subunit), domain 1
Domain ID domain_id1onkA02
Class class4 — Few Secondary Structures
Architecture architecture10 — Irregular
Topology topology470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily10 — Ricin (A Subunit), domain 2
Domain ID domain_id1onkB01
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
Domain ID domain_id1onkB02
Class class2 — Mainly Beta
Architecture architecture80 — Trefoil
Topology topology10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily50 —
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8. Citations (1)

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9. Files and Curves (10)