1k7u

Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex

Method: X-RAY DIFFRACTION

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

agglutinin isolectin 3

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Other combination	Homooligomer	Protein 2 其他Polymer 2	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	AGI3_WHEAT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–186； UniProt 1–186 Author chain B； PDBConstruct 1–186； UniProt 1–186

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	1k7u
Deposition date deposition_date	2001-10-22
Structure title title	Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex
Keywords keywords	Hevein-type fold, 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.

1k7u__assembly_1__model_1

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

Download this curve (.dat)

1k7u__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k7u__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.73 Å
Rg (electron density)	20.28 Å
Total Rg	20.84 Å
Atom count	2404
Residues	340
Excluded volume	40974 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k7u__assembly_1__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 (3)

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d1k7ua1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

Domain ID domain_id	d1k7ua2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

Domain ID domain_id	d1k7ua3
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

Domain ID domain_id	d1k7ua4
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

Domain ID domain_id	d1k7ub1
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

Domain ID domain_id	d1k7ub2
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

Domain ID domain_id	d1k7ub3
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

Domain ID domain_id	d1k7ub4
Class class	g — Small proteins
Fold Fold fold	g.3 — Knottins (small inhibitors, toxins, lectins)
Superfamily Superfamily superfamily	g.3.1 — Plant lectins/antimicrobial peptides
Family Family family	g.3.1.1 — Hevein-like agglutinin (lectin) domain

CATH v4.4 (8 domains)

Domain ID domain_id	1k7uA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

Domain ID domain_id	1k7uA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

Domain ID domain_id	1k7uA03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

Domain ID domain_id	1k7uA04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

Domain ID domain_id	1k7uB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

Domain ID domain_id	1k7uB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

Domain ID domain_id	1k7uB03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

Domain ID domain_id	1k7uB04
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	60 — Wheat Germ Agglutinin (Isolectin 2); domain 1
Homologous superfamily homologous superfamily	10 — Endochitinase-like

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Unit-cell length a length_a	44.720 Å
Unit-cell length b length_b	91.550 Å
Unit-cell length c length_c	44.760 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	110.13 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	8.000 Å
R factor r_factor	—
R_work r_work	0.2420
R_free r_free	0.3060

Description description	agglutinin isolectin 3
Molecular weight formula_weight	18752.9 kDa
Source method src_method	nat
Copy count entity_count	2

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	2493

Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex

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

agglutinin isolectin 3

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

1k7u__assembly_1__model_1

1k7u__assembly_1__model_1 | I(q)

1k7u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (4)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	89

Crystal Structure Analysis of crosslinked-WGA3/GlcNAcbeta1,4GlcNAc complex

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

agglutinin isolectin 3

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

1k7u__assembly_1__model_1

1k7u__assembly_1__model_1 | I(q)

1k7u__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (4)