9kx8

Mistletoe Lectin I from Viscum album complexed with epimer form of lactose

Method: X-RAY DIFFRACTION D_max: 83.8 Å Quality: GOOD

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

Beta-galactoside-specific lectin 1 chain A isoform 1

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	Other combination Homooligomer Protein × 2 其他Polymer 3 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 34–280 Chain B； UniProt 302–564	Not recorded	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 beta-D-galactopyranose-(1-4)-alpha-D-idopyranose × 1 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

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 9KX8	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 construct Different mutation/modification Different oligomeric state 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
1ONK Mistletoe lectin I from viscum album Deposited 2003-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 1–254（254 aa）	Not recorded	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
1ONK Mistletoe lectin I from viscum album Deposited 2003-02-28	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 1–254（254 aa）	Not recorded	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
1PUM Mistletoe lectin I in complex with galactose Deposited 2003-06-25	Different construct 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 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 mutation/modification 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 mutation/modification 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 mutation/modification 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 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 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 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 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 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

9 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	ML1_VISAL
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 1–247； UniProt 34–280 Author chain B； PDBConstruct 1–263； UniProt 302–564

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	9kx8
Deposition date deposition_date	2024-12-06
最后修订 last_revision	2025-01-15
Structure title title	Mistletoe Lectin I from Viscum album complexed with epimer form of lactose
Keywords keywords	Mistletoe, Lectin, MLI, PLANT PROTEIN; PLANT 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	26.30 Å
Radius of gyration Rg (electron density) rg_electron	25.34 Å
Forward intensity I(0) i0	60006700.00
Molecular weight molecular_weight	58464.0 kDa
Excluded volume excluded_volume	72357 Å³
Envelope volume envelope_volume	86408 Å³
Hydration-shell volume shell_volume	28898 Å³
Envelope diameter envelope_diameter	87.5 Å
Shell Rg shell_rg	32.28 Å
Envelope Rg envelope_rg	25.39 Å
Shape Rg shape_rg	25.33 Å
Total Rg total_rg	26.08 Å
Total atoms total_atoms	4098
Residues n_residues	510
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	83.8 Å
Rg (real space) rg_real	26.32 Å
Rg uncertainty (real space) rg_real_error	0.55 Å
I(0) (real space) i0_real	6.0010e+07
I(0) uncertainty (real space) i0_real_error	8.3290e+05
Rg (reciprocal space) rg_reciprocal	26.31 Å
I(0) (reciprocal space) i0_reciprocal	60010000.0000
Solution quality estimate total_estimate	0.8967
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.9 Å
Skewness Skewness skewness	0.364
Kurtosis Kurtosis kurtosis	-0.411
Angular range angular_range	— – 0.3000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	10420000.0000
Real-space data points n_real_points	61
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.909; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.988; Smooth: 0.938

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Description description	Beta-galactoside-specific lectin 1 chain A isoform 1
Molecular weight formula_weight	27357.8 kDa
EC 编号 ec_number	3.2.2.22
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4142

YERLRLRVTHQTTGAEYFSFITLLRDYVSSGSFSNEIPLLSQSTIPVSDAARFVLVELTNEGGDSITAAIDVTNLYVVAYQAGDQSYFLRDAPRGGETHLFTGTTKSALPFNGSYPDLERYAGHRDQVPLGIDQLIQSVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIRLALSPGNFVTLTNVRDVIASLAIMLFVC

Entity 2 Entity 2 polymer

Description description	Beta-galactoside-specific lectin 1 chain B
Molecular weight formula_weight	28467.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

ADVTCSASEPTVRIVGRNGMCVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATLWEIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGHADLCMESNGGSVHVETCVASQQNQRWALYGDGSIRPKQNQDQCLTCGRDSVSTVINIVSCSAGSSGQRWVFTNEGAILNLKNGLAMDVAQANPALARIIIYPATGKPNQMWLPVP

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	2

Entity 4 Entity 4 branched

Description description	beta-D-galactopyranose-(1-4)-alpha-D-idopyranose
Molecular weight formula_weight	342.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	5

Entity 6 Entity 6 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 7 Entity 7 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 8 Entity 8 non-polymer

Description description	GLYCINE
Molecular weight formula_weight	75.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	nat
Copy count entity_count	2

Entity 10 Entity 10 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 11 Entity 11 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	44

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8. Citations (1)

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Unit-cell length a length_a	107.859 Å
Unit-cell length b length_b	107.859 Å
Unit-cell length c length_c	311.386 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	P 65 2 2
Space-group number int_tables_number	179
Crystal system crystal_system	hexagonal

Resolution resolution	2.280 Å
Low-resolution limit resolution_low	40.770 Å
R factor r_factor	0.2106
R_work r_work	0.2095
R_free r_free	0.2312

fit	/app/data/saxs_computation/kx/9kx8/9kx8.fit
pddf	/app/data/pr_computation/kx/9kx8/9kx8.pr.out
profile	/app/data/saxs_computation/kx/9kx8/9kx8.dat

Mistletoe Lectin I from Viscum album complexed with epimer form of lactose

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

Beta-galactoside-specific lectin 1 chain A isoform 1

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

6. Entities and Polymers Entities & Polymers (11)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 non-polymer

Entity 11 Entity 11 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)