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2d3s

Crystal Structure of basic winged bean lectin with Tn-antigen

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Basic agglutinin

OrganismNot specified

UniProt O24313

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

Other States of the Same Protein in the Database

Monomer

None

Homodimer
1wbf

1 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1wbl 1wbl 2d3s 2d3s 2dtw 2dtw 2dty 2dty 2du0 2du0 2du1 2du1

38 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name LEC1_PSOTE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–242； UniProt 1–242 Author chain B； PDBConstruct 1–242； UniProt 1–242 Author chain C； PDBConstruct 1–242； UniProt 1–242 Author chain D； PDBConstruct 1–242； UniProt 1–242

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_id2d3s
Deposition date deposition_date2005-10-01
Structure title titleCrystal Structure of basic winged bean lectin with Tn-antigen
Keywords keywordsLegume lectin, GLYCOSYLATED PROTEIN, AGGLUTININ, TN-ANTIGEN, SUGAR BINDING PROTEIN; SUGAR BINDING PROTEIN
Experimental Method methodX-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.

2d3s__assembly_1__model_1

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

Download this curve (.dat)

2d3s__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2d3s__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）26.24 Å
Rg (electron density)24.98 Å
Total Rg25.92 Å
Atom count3854
Residues474
Excluded volume68648 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2d3s__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2d3s__assembly_2__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 (10)

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2d3sa_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins
Domain ID domain_idd2d3sb_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins
Domain ID domain_idd2d3sc_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins
Domain ID domain_idd2d3sd_
Class classb — All beta proteins
Fold Fold foldb.29 — Concanavalin A-like lectins/glucanases
Superfamily Superfamily superfamilyb.29.1 — Concanavalin A-like lectins/glucanases
Family Family familyb.29.1.1 — Legume lectins

CATH v4.4 (4 domains)

Domain ID domain_id2d3sA00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id2d3sB00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id2d3sC00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
Domain ID domain_id2d3sD00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily200 —
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7. Citations (4)