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3e80

Structure of Heparinase II complexed with heparan sulfate degradation disaccharide product

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

Heparinase II protein

OrganismNot specified

UniProt Q46080

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Other combination Monomer Protein 1 其他Polymer 2 alpha-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose × 1 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 ZINC ION × 1 PHOSPHATE ION × 4 water × 1 Consistent with protein count
2 Other combination Monomer Protein 1 其他Polymer 2 alpha-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose × 1 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 ZINC ION × 1 PHOSPHATE ION × 3 water × 1 Consistent with protein count
3 Other combination Monomer Protein 1 其他Polymer 2 alpha-D-xylopyranose-(1-4)-alpha-D-glucopyranuronic acid-(1-2)-[alpha-L-rhamnopyranose-(1-4)]alpha-D-mannopyranose × 1 4-deoxy-alpha-L-threo-hex-4-enopyranuronic acid-(1-4)-2-acetamido-2-deoxy-alpha-D-glucopyranose × 1 ZINC ION × 1 PHOSPHATE ION × 2 water × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2fut 3e7j 3e80 3e80 3e80

5 assemblies

View Construct and Data Evidence
UniProt name Q46080_PEDHE
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–749； UniProt 24–772 Author chain B； PDBConstruct 1–749； UniProt 24–772 Author chain C； PDBConstruct 1–749； UniProt 24–772

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_id3e80
Deposition date deposition_date2008-08-19
Structure title titleStructure of Heparinase II complexed with heparan sulfate degradation disaccharide product
Keywords keywordsalpha and beta lyase fold, alpha6/alpha6 incomplete toroid, SUGAR BINDING PROTEIN, LYASE; SUGAR BINDING PROTEIN, LYASE
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.

3e80__assembly_2__model_1

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

Download this curve (.dat)

3e80__assembly_2__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3e80__assembly_2__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）28.71 Å
Rg (electron density)28.37 Å
Total Rg29.22 Å
Atom count6061
Residues746
Excluded volume108030 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3e80__assembly_1__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3e80__assembly_2__model_1 monomeric （1） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 3e80__assembly_3__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 (6)

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6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id3e80A01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily100 — Chondroitin AC/alginate lyase
Domain ID domain_id3e80A02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily70 —
Domain ID domain_id3e80A03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2750 —
Domain ID domain_id3e80B01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily100 — Chondroitin AC/alginate lyase
Domain ID domain_id3e80B02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily70 —
Domain ID domain_id3e80B03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2750 —
Domain ID domain_id3e80C01
Class class1 — Mainly Alpha
Architecture architecture50 — Alpha/alpha barrel
Topology topology10 — Glycosyltransferase
Homologous superfamily homologous superfamily100 — Chondroitin AC/alginate lyase
Domain ID domain_id3e80C02
Class class2 — Mainly Beta
Architecture architecture70 — Distorted Sandwich
Topology topology98 — Beta-galactosidase; Chain A, domain 5
Homologous superfamily homologous superfamily70 —
Domain ID domain_id3e80C03
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily2750 —
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7. Citations (1)