3ca6

Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen

Method: X-RAY DIFFRACTION

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

Agglutinin II

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Monomer	Protein 1 其他Polymer 3	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 SULFATE ION × 4 ACETATE ION × 1 SERINE × 1 water × 1	Consistent with protein count
2	Other combination	Homooligomer	Protein 2 其他Polymer 6	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 SULFATE ION × 8 ACETATE ION × 2 SERINE × 2 water × 2	Consistent with protein count
3	Other combination	Homooligomer	Protein 2 其他Polymer 6	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 SULFATE ION × 8 ACETATE ION × 2 SERINE × 2 water × 2	Consistent with protein count
4	Other combination	Homooligomer	Protein 2 其他Polymer 6	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 4 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 2 2-acetamido-2-deoxy-alpha-D-galactopyranose × 2 SULFATE ION × 8 ACETATE ION × 2 SERINE × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	NIGB_SAMNI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–258； UniProt 306–563

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	3ca6
Deposition date deposition_date	2008-02-19
Structure title title	Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen
Keywords keywords	BETA-TREFOIL, RICIN-B DOMAIN, GLYCOSYLATION, LECTIN, Glycoprotein, SUGAR BINDING PROTEIN, Plant Protein; SUGAR BINDING PROTEIN, Plant Protein
Experimental Method method	X-RAY DIFFRACTION

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3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

3ca6__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3ca6__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3ca6__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.90 Å
Rg (electron density)	20.06 Å
Total Rg	20.97 Å
Atom count	2143
Residues	257
Excluded volume	37762 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3ca6__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3ca6__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3ca6__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3ca6__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	Agglutinin II
Molecular weight formula_weight	28439.1 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	2635

TSFTRNIVGRDGLCVDVRNGYDTDGTPLQLWPCGTQRNQRWTFDSDDTIRSMGKCMTANGLNNGSNIVIFNCSTAAENAIKWEVPIDGSIINPSSGLVMTAPRAASRTILLLEDNIYAASQGWTVTNNVKPIVASIVGYKEMCLQSNGENNGVWMEDCEATSLQQQWALYGDRTIRVNSTRGLCVTTNGYNSKDLIIILKCQGLPSQRWFFNSDGAIVNPKSRLVMDVRASNVSLREIIIFPATGNPNQQWVTQVLPS

Entity 2 Entity 2 branched

Description description	alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	570.5 kDa
Source method src_method	man
Copy count entity_count	2

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	1

Entity 4 Entity 4 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	1

Entity 5 Entity 5 non-polymer

Description description	2-acetamido-2-deoxy-alpha-D-galactopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 8 Entity 8 non-polymer

Description description	SERINE
Molecular weight formula_weight	105.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	339

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3ca6a1
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.42.2.0 — automated matches

Domain ID domain_id	d3ca6a2
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.42.2.0 — automated matches

CATH v4.4 (2 domains)

Domain ID domain_id	3ca6A01
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	3ca6A02
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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Unit-cell length a length_a	127.042 Å
Unit-cell length b length_b	127.042 Å
Unit-cell length c length_c	75.492 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	I 41 2 2
Space-group number int_tables_number	98
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1433
R_work r_work	0.1409
R_free r_free	0.1873

Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen

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

Agglutinin II

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ca6__assembly_1__model_1

3ca6__assembly_1__model_1 | I(q)

3ca6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Sambucus nigra agglutinin II (SNA-II)- tetragonal crystal form- complexed to Tn antigen

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

Agglutinin II

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3ca6__assembly_1__model_1

3ca6__assembly_1__model_1 | I(q)

3ca6__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

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 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)