SAXSdb — 2mll

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

PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)

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 heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 5–264	Not recorded	PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II) × 1 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

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 2MLL	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	Parsed fields agree	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 construct 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
1ONK Mistletoe lectin I from viscum album Deposited 2003-02-28	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain B 1–264（264 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 ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–264（264 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

3 other PDB entries and 4 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 1–255； UniProt 5–264

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2mll
Deposition date deposition_date	1999-03-16
Structure title title	MISTLETOE LECTIN I FROM VISCUM ALBUM
Keywords keywords	RIBOSOME-INACTIVATING PROTEIN TYPE II, RIBOSOME; RIBOSOME
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	25.75 Å
Radius of gyration Rg (electron density) rg_electron	24.89 Å
Forward intensity I(0) i0	49055600.00
Molecular weight molecular_weight	53266.0 kDa
Excluded volume excluded_volume	66140 Å³
Envelope volume envelope_volume	78287 Å³
Hydration-shell volume shell_volume	26896 Å³
Envelope diameter envelope_diameter	86.0 Å
Shell Rg shell_rg	31.47 Å
Envelope Rg envelope_rg	24.98 Å
Shape Rg shape_rg	24.89 Å
Total Rg total_rg	25.58 Å
Total atoms total_atoms	3748
Residues n_residues	496
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	83.1 Å
Rg (real space) rg_real	25.79 Å
Rg uncertainty (real space) rg_real_error	0.54 Å
I(0) (real space) i0_real	4.9060e+07
I(0) uncertainty (real space) i0_real_error	6.6780e+05
Rg (reciprocal space) rg_reciprocal	25.78 Å
I(0) (reciprocal space) i0_reciprocal	49060000.0000
Solution quality estimate total_estimate	0.8945
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.8 Å
Skewness Skewness skewness	0.393
Kurtosis Kurtosis kurtosis	-0.379
Angular range angular_range	— – 0.3100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	9133000.0000
Real-space data points n_real_points	63
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.894; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.987; Smooth: 0.956

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)
Molecular weight formula_weight	25656.7 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	3963

YERGDLDVTAQTTGAGYFSFITLLRDYVSSGSFSNAIPLLSQSGGGGEAGRFVLVELTNSGGDGITVAIDVTNLYVVAYQAGSQSYFLSGPGGRGGFTGTTRSSLPFNGSYPDLEQYGGQRKQIPLGIDQLIQSVTALKFPGSTRTGARSILILIQMISEAARFNPILWRARQYINSGASFLPDVYMLELETSWGQQSTQVQHSTDGVFNNPIALADPGGGVTLTNVRDVIASLAIMLFVC

Entity 2 Entity 2 polymer

Description description	PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)
Molecular weight formula_weight	27072.1 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

CSASEPTVRIVGRNGMNVDVRDDDFHDGNQIQLWPSKSNNDPNQLWTIKRDGTIRSNGSCLTTYGYTAGVYVMIFDCATAVGEATVWQIWGNGTIINPRSNLVLAASSGIKGTTLTVQTLDYTLGQGWLAGNDTAPREVTIYGFNDLCMESGGGSVTVETCSSGKADKWALYGDGSIRPEQNQAQCLTSGGDSVAGVNIVSCSGAASGQRWVFTNEGAILNLKNGLAMDVANPGGGRIIIYPATGKPNQMWLPVF

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	man
Copy count entity_count	3

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	215

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7. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (3 domains)

Domain ID domain_id	d2mlla_
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	d2mllb1
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	d2mllb2
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	2mllA01
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	2mllA02
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	2mllB01
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	2mllB02
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	107.648 Å
Unit-cell length b length_b	107.648 Å
Unit-cell length c length_c	311.278 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	2.700 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2510
R_free r_free	0.3190

fit	/app/data/saxs_computation/ml/2mll/2mll.fit
pddf	/app/data/pr_computation/ml/2mll/2mll.pr.out
profile	/app/data/saxs_computation/ml/2mll/2mll.dat

MISTLETOE LECTIN I FROM VISCUM ALBUM

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

PROTEIN (RIBOSOME-INACTIVATING PROTEIN TYPE II)

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 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)