2zmk

Crystl structure of Basic Winged bean lectin in complex with Gal-alpha-1,4-Gal-Beta-Ethylene

Method: X-RAY DIFFRACTION

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

Basic agglutinin

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 6	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside × 2 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 2 CALCIUM ION × 2 water × 2	Consistent with protein count
2	Other combination	Homooligomer	Protein 2 其他Polymer 5	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside × 2 MANGANESE (II) ION × 2 CALCIUM ION × 2 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose × 1 water × 2	Consistent with protein count
3	Other combination	Monomer	Protein 1 其他Polymer 3	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside × 1 MANGANESE (II) ION × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
4	Other combination	Monomer	Protein 1 其他Polymer 3	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside × 1 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 MANGANESE (II) ION × 1 CALCIUM ION × 1 water × 1	Consistent with protein count
5	Other combination	Monomer	Protein 1 其他Polymer 2	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside × 1 MANGANESE (II) ION × 1 CALCIUM ION × 1 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 beta-D-mannopyranose × 1 water × 1	Consistent with protein count
6	Other combination	Monomer	Protein 1 其他Polymer 3	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-L-fucopyranose-(1-3)-[2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)]2-acetamido-2-deoxy-beta-D-glucopyranose × 1 alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside × 1 MANGANESE (II) ION × 1 CALCIUM ION × 1 water × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	LEC1_PSOTE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–241； UniProt 2–242 Author chain B； PDBConstruct 1–241； UniProt 2–242 Author chain C； PDBConstruct 1–241； UniProt 2–242 Author chain D； PDBConstruct 1–241； UniProt 2–242

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	2zmk
Deposition date deposition_date	2008-04-19
Structure title title	Crystl structure of Basic Winged bean lectin in complex with Gal-alpha-1,4-Gal-Beta-Ethylene
Keywords keywords	Legume Lectin, Sugar binding Protein, Sugar Specificity, Glycoprotein, Lectin; 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.

2zmk__assembly_1__model_1

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

Download this curve (.dat)

2zmk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zmk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.02 Å
Rg (electron density)	24.76 Å
Total Rg	25.66 Å
Atom count	3804
Residues	474
Excluded volume	67704 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zmk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zmk__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2zmk__assembly_3__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2zmk__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2zmk__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2zmk__assembly_6__model_1`	monomeric （1）	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 (10)

Entity 1 Entity 1 polymer

Description description	Basic agglutinin
Molecular weight formula_weight	26505.6 kDa
Source method src_method	nat
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	7739

KTISFNFNQFHQNEEQLKLQRDARISSNSVLELTKVVNGVPTWNSTGRALYAKPVQVWDSTTGNVASFETRFSFSIRQPFPRPHPADGLVFFIAPPNTQTGEGGGYFGIYNPLSPYPFVAVEFDTFRNTWDPQIPHIGIDVNSVISTKTVPFTLDNGGIANVVIKYDASTKILHVVLVFPSLGTIYTIADIVDLKQVLPESVNVGFSAATGDPSGKQRNATETHDILSWSFSASLPGTNEF

Entity 2 Entity 2 branched

Description description	alpha-L-fucopyranose-(1-3)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	367.3 kDa
Source method src_method	man
Copy count entity_count	4

Entity 3 Entity 3 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 4 Entity 4 branched

Description description	alpha-D-galactopyranose-(1-4)-ethyl beta-D-galactopyranoside
Molecular weight formula_weight	370.4 kDa
Source method src_method	man
Copy count entity_count	4

Entity 5 Entity 5 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 6 Entity 6 non-polymer

Description description	MANGANESE (II) ION
Molecular weight formula_weight	54.9 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 7 Entity 7 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 8 Entity 8 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 9 Entity 9 non-polymer

Description description	beta-D-mannopyranose
Molecular weight formula_weight	180.2 kDa
Source method src_method	man
Copy count entity_count	1

Entity 10 Entity 10 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	171

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2zmka_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

Domain ID domain_id	d2zmkb_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

Domain ID domain_id	d2zmkc_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

Domain ID domain_id	d2zmkd_
Class class	b — All beta proteins
Fold Fold fold	b.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamily	b.29.1 — Concanavalin A-like lectins/glucanases
Family Family family	b.29.1.1 — Legume lectins

CATH v4.4 (4 domains)

Domain ID domain_id	2zmkA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2zmkB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2zmkC00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	200 —

Domain ID domain_id	2zmkD00
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	156.921 Å
Unit-cell length b length_b	89.958 Å
Unit-cell length c length_c	73.321 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	P 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	29.630 Å
R factor r_factor	0.2170
R_work r_work	0.2170
R_free r_free	0.2560

Crystl structure of Basic Winged bean lectin in complex with Gal-alpha-1,4-Gal-Beta-Ethylene

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

Basic agglutinin

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

2zmk__assembly_1__model_1

2zmk__assembly_1__model_1 | I(q)

2zmk__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)

Crystl structure of Basic Winged bean lectin in complex with Gal-alpha-1,4-Gal-Beta-Ethylene

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

Basic agglutinin

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

2zmk__assembly_1__model_1

2zmk__assembly_1__model_1 | I(q)

2zmk__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 (10)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 branched

Entity 3 Entity 3 branched

Entity 4 Entity 4 branched

Entity 5 Entity 5 branched

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 non-polymer

Entity 10 Entity 10 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (3)