SAXSdb — 5jm1

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

Agglutinin alpha chain

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Agglutinin beta-3 chain × 2 （P18673） 1,2-ETHANEDIOL × 5 DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 1	Agglutinin beta-3 chain × 2 （P18673） alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose × 1 1,2-ETHANEDIOL × 5 methyl alpha-D-galactopyranoside × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LECA_ARTIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–133； UniProt 1–133 Author chain C； PDBConstruct 1–133； UniProt 1–133 Author chain E； PDBConstruct 1–133； UniProt 1–133 Author chain G； PDBConstruct 1–133； UniProt 1–133

Agglutinin beta-3 chain

OrganismNot specified

UniProt P18673

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	Agglutinin alpha chain × 2 （P18670） 1,2-ETHANEDIOL × 5 DI(HYDROXYETHYL)ETHER × 1 water × 4	Consistent with protein count
2	Other combination	Heteromer	Protein 4 其他Polymer 1	Agglutinin alpha chain × 2 （P18670） alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose × 1 1,2-ETHANEDIOL × 5 methyl alpha-D-galactopyranoside × 1 water × 4	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LECB3_ARTIN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–19； UniProt 2–20 Author chain D； PDBConstruct 1–19； UniProt 2–20 Author chain F； PDBConstruct 1–19； UniProt 2–20 Author chain H； PDBConstruct 1–19； UniProt 2–20

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	5jm1
Deposition date deposition_date	2016-04-28
Structure title title	Structure of tetrameric jacalin complexed with a trisaccharide, Gal alpha-(1,3) Gal beta-(1,4) Gal
Keywords keywords	;Plant lectins, sugar binding protein, Galactose specific lectin, beta-prism I fold, post translational proteolysis, T-antigen binding protein, reducing, non-reducing sugars ;; 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.

5jm1__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

5jm1__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5jm1__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	21.05 Å
Rg (electron density)	19.89 Å
Total Rg	20.84 Å
Atom count	2344
Residues	296
Excluded volume	42075 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5jm1__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5jm1__assembly_2__model_1`	tetrameric （4）	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 (7)

Entity 1 Entity 1 polymer

Description description	Agglutinin alpha chain
Molecular weight formula_weight	14673.5 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G
Atom count atom_count	5041

GKAFDDGAFTGIREINLSYNKETAIGDFQVVYDLNGSPYVGQNHKSFITGFTPVKISLDFPSEYIMEVSGYTGNVSGYVVVRSLTFKTNKKTYGPYGVTSGTPFNLPIENGLIVGFKGSIGYWLDYFSMYLSL

Entity 2 Entity 2 polymer

Description description	Agglutinin beta-3 chain
Molecular weight formula_weight	1944.2 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H

EQSGISQTVIVGPWGAKVS

Entity 3 Entity 3 branched

Description description	alpha-D-galactopyranose-(1-3)-beta-D-galactopyranose-(1-4)-beta-D-galactopyranose
Molecular weight formula_weight	504.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	10

Entity 5 Entity 5 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	methyl alpha-D-galactopyranoside
Molecular weight formula_weight	194.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	403

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	5jm1A00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	5jm1C00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	5jm1E00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

Domain ID domain_id	5jm1G00
Class class	2 — Mainly Beta
Architecture architecture	100 — Aligned Prism
Topology topology	10 — Vitelline Membrane Outer Layer Protein I, subunit A
Homologous superfamily homologous superfamily	30 — Jacalin-like lectin domain

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Unit-cell length a length_a	58.490 Å
Unit-cell length b length_b	81.580 Å
Unit-cell length c length_c	63.000 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.65 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	46.010 Å
R factor r_factor	0.1862
R_work r_work	0.1804
R_free r_free	0.2374

Structure of tetrameric jacalin complexed with a trisaccharide, Gal alpha-(1,3) Gal beta-(1,4) Gal

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

Agglutinin alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Agglutinin beta-3 chain

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

5jm1__assembly_2__model_1

5jm1__assembly_2__model_1 | I(q)

5jm1__assembly_2__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Structure of tetrameric jacalin complexed with a trisaccharide, Gal alpha-(1,3) Gal beta-(1,4) Gal

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

Agglutinin alpha chain

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Agglutinin beta-3 chain

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

5jm1__assembly_2__model_1

5jm1__assembly_2__model_1 | I(q)

5jm1__assembly_2__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 (7)

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 non-polymer

Entity 7 Entity 7 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)