SAXSdb — 4d69

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

LECTIN

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
10	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
11	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
12	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
2	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
3	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
4	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
5	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
6	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
7	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
8	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count
9	Other combination	Heteromer	Protein 2 其他Polymer 1	SHORT ANTIGEN PEPTIDE × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 2-acetamido-2-deoxy-alpha-D-galactopyranose × 1 MANGANESE (II) ION × 2 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEC_SOYBN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–253； UniProt 33–285 Author chain B； PDBConstruct 1–253； UniProt 33–285 Author chain C； PDBConstruct 1–253； UniProt 33–285 Author chain D； PDBConstruct 1–253； UniProt 33–285 Author chain E； PDBConstruct 1–253； UniProt 33–285 Author chain F； PDBConstruct 1–253； UniProt 33–285 Author chain G； PDBConstruct 1–253； UniProt 33–285 Author chain H； PDBConstruct 1–253； UniProt 33–285 Author chain I； PDBConstruct 1–253； UniProt 33–285 Author chain J； PDBConstruct 1–253； UniProt 33–285 Author chain K； PDBConstruct 1–253； UniProt 33–285 Author chain L； PDBConstruct 1–253； UniProt 33–285

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	4d69
Deposition date deposition_date	2014-11-10
Structure title title	SOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn
Keywords keywords	SUGAR-BINDING PROTEIN, SUGAR BINDING PROTEIN; SUGAR BINDING 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.

4d69__assembly_10__model_1

Assembly 10 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

4d69__assembly_10__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4d69__assembly_10__model_1 | P(r) · Pending

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

Rg（Guinier）	18.27 Å
Rg (electron density)	17.04 Å
Total Rg	18.11 Å
Atom count	1886
Residues	238
Excluded volume	33503 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4d69__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4d69__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4d69__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`4d69__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`4d69__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`4d69__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`4d69__assembly_7__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`4d69__assembly_8__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`4d69__assembly_9__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
10	1	`4d69__assembly_10__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
11	1	`4d69__assembly_11__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
12	1	`4d69__assembly_12__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 (6)

Entity 1 Entity 1 polymer

Description description	LECTIN
Molecular weight formula_weight	27595.8 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F,G,H,I,J,K,L
Atom count atom_count	22512

AETVSFSWNKFVPKQPNMILQGDAIVTSSGKLQLNKVDENGTPKPSSLGRALYSTPIHIWDKETGSVASFAASFNFTFYAPDTKRLADGLAFFLAPIDTKPQTHAGYLGLFNENESGDQVVAVEFDTFRNSWDPPNPHIGINVNSIRSIKTTSWDLANNKVAKVLITYDASTSLLVASLVYPSQRTSNILSDVVDLKTSLPEWVRIGFSAATGLDIPGESHDVLSWSFASNLPHASSNIDPLDLTSFVLHEAI

Entity 2 Entity 2 polymer

Description description	SHORT ANTIGEN PEPTIDE
Molecular weight formula_weight	559.6 kDa
Source method src_method	nat
Copy count entity_count	12

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,P,Q,R,S,T,U,V,W,X,Y,Z

APDTR

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	12

Entity 4 Entity 4 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	12

Entity 5 Entity 5 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	24

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	118

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6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

Domain ID domain_id	4d69A00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69B00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69C00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69D00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69E00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69F00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69G00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69H00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69I00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69J00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69K00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	4d69L00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

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Unit-cell length a length_a	114.232 Å
Unit-cell length b length_b	114.232 Å
Unit-cell length c length_c	202.893 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	36

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.700 Å
Low-resolution limit resolution_low	202.890 Å
R factor r_factor	0.2315
R_work r_work	0.2302
R_free r_free	0.2743

SOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn

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

LECTIN

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

4d69__assembly_10__model_1

4d69__assembly_10__model_1 | I(q)

4d69__assembly_10__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)

SOYBEAN AGGLUTININ FROM GLYCINE MAX IN COMPLEX WITH THE ANTIGEN Tn

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

LECTIN

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

4d69__assembly_10__model_1

4d69__assembly_10__model_1 | I(q)

4d69__assembly_10__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 branched

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 12 domains

CATH v4.4 (12 domains)

7. Citations (1)