SAXSdb — 1sz6

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

RRNA N-GLYCOSIDASE A CHAIN

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 34–282 Chain B； UniProt 302–564	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

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 1SZ6	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 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
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 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 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 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 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 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 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 1–249； UniProt 34–282 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1sz6
Deposition date deposition_date	2004-04-04
Structure title title	MISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A RESOLUTION
Keywords keywords	RIBOSOME-INACTIVATING PROTEIN TYPE II, HYDROLASE INHIBITOR; HYDROLASE INHIBITOR
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	26.05 Å
Radius of gyration Rg (electron density) rg_electron	25.18 Å
Forward intensity I(0) i0	58568300.00
Molecular weight molecular_weight	58139.0 kDa
Excluded volume excluded_volume	72117 Å³
Envelope volume envelope_volume	82817 Å³
Hydration-shell volume shell_volume	27977 Å³
Envelope diameter envelope_diameter	86.3 Å
Shell Rg shell_rg	31.93 Å
Envelope Rg envelope_rg	25.27 Å
Shape Rg shape_rg	25.16 Å
Total Rg total_rg	25.91 Å
Total atoms total_atoms	4079
Residues n_residues	512
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	84.0 Å
Rg (real space) rg_real	26.08 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	5.8570e+07
I(0) uncertainty (real space) i0_real_error	7.3130e+05
Rg (reciprocal space) rg_reciprocal	26.07 Å
I(0) (reciprocal space) i0_reciprocal	58570000.0000
Solution quality estimate total_estimate	0.8941
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	27.6 Å
Skewness Skewness skewness	0.384
Kurtosis Kurtosis kurtosis	-0.379
Angular range angular_range	— – 0.3050 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8857000.0000
Real-space data points n_real_points	62
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.896; 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 (8)

Entity 1 Entity 1 polymer

Description description	RRNA N-GLYCOSIDASE A CHAIN
Molecular weight formula_weight	27226.6 kDa
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	4397

YERLSLRTVQQTTGAEYFSFITLLRDFVSSGSFSNNIPLLRQSTIPVSEGSRFVLVELTNAGGDSITAAIDVTNLYVVAYQAGQQSYFLKDAPAGAETQDFAGTTRSSLPFNGSYPDLERYAGHRDQIPLGIDQLIASVTALRFPGGSTRTQARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIALALPPGNVVTLTNIRDVIASLAIMLFVCGE

Entity 2 Entity 2 polymer

Description description	BETA-GALACTOSIDE SPECIFIC LECTIN I B CHAIN
Molecular weight formula_weight	28465.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

DDVTCSASEPIVRIVGRNGMTVDVRDDDFQDGNQIQLWPSKSNNDPNQLWTIKKDGTIRSNGSCLTTYGYTAGVYVMIFDCNTAVREATIWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFRDLCMESAGGSVWVETCTAGQENQRWALYGDGSIRPKQNQSQCLTNGRDSVSTVINIVSCSAGSSGQRWVFTNAGAILNLKNGLAMDVAQANPALARIIIYPATGNPNQMWLPVP

Entity 3 Entity 3 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	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	1

Entity 5 Entity 5 non-polymer

Description description	AZIDE ION
Molecular weight formula_weight	42.0 kDa
Source method src_method	syn
Copy count entity_count	3

Entity 6 Entity 6 non-polymer

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

Entity 7 Entity 7 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	15

Entity 8 Entity 8 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	318

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d1sz6a_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.165 — Ribosome inactivating proteins (RIP)
Superfamily Superfamily superfamily	d.165.1 — Ribosome inactivating proteins (RIP)
Family Family family	d.165.1.1 — Plant cytotoxins

Domain ID domain_id	d1sz6b1
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

Domain ID domain_id	d1sz6b2
Class class	b — All beta proteins
Fold Fold fold	b.42 — beta-Trefoil
Superfamily Superfamily superfamily	b.42.2 — Ricin B-like lectins
Family Family family	b.42.2.1 — Ricin B-like

CATH v4.4 (4 domains)

Domain ID domain_id	1sz6A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	420 — Ricin (A subunit); domain 1
Homologous superfamily homologous superfamily	10 — Ricin (A subunit), domain 1

Domain ID domain_id	1sz6A02
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	470 — Ricin (A Subunit), domain 2
Homologous superfamily homologous superfamily	10 — Ricin (A Subunit), domain 2

Domain ID domain_id	1sz6B01
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1sz6B02
Class class	2 — Mainly Beta
Architecture architecture	80 — Trefoil
Topology topology	10 — Trefoil (Acidic Fibroblast Growth Factor, subunit A)
Homologous superfamily homologous superfamily	50 —

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8. Citations (1)

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Unit-cell length a length_a	106.880 Å
Unit-cell length b length_b	106.880 Å
Unit-cell length c length_c	310.740 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	—

Resolution resolution	2.050 Å
Low-resolution limit resolution_low	29.000 Å
R factor r_factor	0.2110
R_work r_work	0.2110
R_free r_free	0.2530

fit	/app/data/saxs_computation/sz/1sz6/1sz6.fit
pddf	/app/data/pr_computation/sz/1sz6/1sz6.pr.out
profile	/app/data/saxs_computation/sz/1sz6/1sz6.dat

MISTLETOE LECTIN I FROM VISCUM ALBUM. CRYSTAL STRUCTURE AT 2.05 A RESOLUTION

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

RRNA N-GLYCOSIDASE A CHAIN

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 (8)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 water

7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

CATH v4.4 (4 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)