SAXSdb — 4r6p

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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 8	Agglutinin beta-3 chain × 4 （P18673） ISOPROPYL ALCOHOL × 4 1,2-ETHANEDIOL × 1 4-METHYL-2H-CHROMEN-2-ONE × 1 beta-D-galactopyranose × 1 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Agglutinin beta-3 chain × 2 （P18673） ISOPROPYL ALCOHOL × 3 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Agglutinin beta-3 chain × 2 （P18673） ISOPROPYL ALCOHOL × 1 4-METHYL-2H-CHROMEN-2-ONE × 1 beta-D-galactopyranose × 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 8	Agglutinin alpha chain × 4 （P18670） ISOPROPYL ALCOHOL × 4 1,2-ETHANEDIOL × 1 4-METHYL-2H-CHROMEN-2-ONE × 1 beta-D-galactopyranose × 1 water × 8	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 4	Agglutinin alpha chain × 2 （P18670） ISOPROPYL ALCOHOL × 3 1,2-ETHANEDIOL × 1 water × 4	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 4	Agglutinin alpha chain × 2 （P18670） ISOPROPYL ALCOHOL × 1 4-METHYL-2H-CHROMEN-2-ONE × 1 beta-D-galactopyranose × 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	4r6p
Deposition date deposition_date	2014-08-26
Structure title title	Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.
Keywords keywords	;Galactose specific lectin, beta-prism I fold, post translational proteolysis, T-antigen binding protein, Plant lectins, Galactose, 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.

4r6p__assembly_1__model_1

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

Download this curve (.dat)

4r6p__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4r6p__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.44 Å
Rg (electron density)	26.53 Å
Total Rg	27.24 Å
Atom count	4596
Residues	594
Excluded volume	82456 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4r6p__assembly_1__model_1`	octameric （8）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4r6p__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`4r6p__assembly_3__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	5071

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 non-polymer

Description description	ISOPROPYL ALCOHOL
Molecular weight formula_weight	60.1 kDa
Source method src_method	syn
Copy count entity_count	4

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	1

Entity 5 Entity 5 non-polymer

Description description	4-METHYL-2H-CHROMEN-2-ONE
Molecular weight formula_weight	160.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 non-polymer

Description description	beta-D-galactopyranose
Molecular weight formula_weight	180.2 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	475

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	4r6pA00
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	4r6pC00
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	4r6pE00
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	4r6pG00
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	58.530 Å
Unit-cell length b length_b	80.880 Å
Unit-cell length c length_c	63.040 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	107.88 °
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	1.700 Å
Low-resolution limit resolution_low	30.630 Å
R factor r_factor	0.1683
R_work r_work	0.1660
R_free r_free	0.2113

Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.

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

4r6p__assembly_1__model_1

4r6p__assembly_1__model_1 | I(q)

4r6p__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (6)

Jacalin-carbohydrate interactions. Distortion of the ligand as a determinant of affinity.

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

4r6p__assembly_1__model_1

4r6p__assembly_1__model_1 | I(q)

4r6p__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 (7)

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 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (6)