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2qho

Crystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin

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

Ubiquitin

OrganismNot specified

UniProt P62990

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 E3 ubiquitin-protein ligase EDD1 × 1 （O95071） water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 E3 ubiquitin-protein ligase EDD1 × 1 （O95071） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 E3 ubiquitin-protein ligase EDD1 × 1 （O95071） water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 E3 ubiquitin-protein ligase EDD1 × 1 （O95071） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1p3q 1v80 1v81 3h1u 3h1u

5 assemblies

Homodimer
1aar 3m3j 3m3j 3m3j

4 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1p3q 1wr6 1wr6 1wr6 1wr6 1wrd 1wrd 1yd8 1yd8 2c7m 2c7n 2c7n

31 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBIQ_BOVIN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–76； UniProt 1–76 Author chain C； PDBConstruct 1–76； UniProt 1–76 Author chain E； PDBConstruct 1–76； UniProt 1–76 Author chain G； PDBConstruct 1–76； UniProt 1–76

E3 ubiquitin-protein ligase EDD1

Homo sapiens

UniProt O95071

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P62990） water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P62990） water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P62990） water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Ubiquitin × 1 （P62990） water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1i2t 3pt3 3pt3

3 assemblies

Homodimer
8bja 8d4x 8e0q 8p82

4 assemblies

Homotetramer
8ewi 8p83

2 assemblies

Other homooligomers
8c06

1 assemblies

Heteromeric or nucleic-acid complex
2qho 2qho 2qho 2qho 8c07

5 assemblies

View Construct and Data Evidence
UniProt name EDD1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 3–53； UniProt 180–230 Author chain D； PDBConstruct 3–53； UniProt 180–230 Author chain F； PDBConstruct 3–53； UniProt 180–230 Author chain H； PDBConstruct 3–53； UniProt 180–230

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_id2qho
Deposition date deposition_date2007-07-02
Structure title titleCrystal structure of the UBA domain from EDD ubiquitin ligase in complex with ubiquitin
Keywords keywordsprotein-protein complex, protein binding-ligase COMPLEX; protein binding/ligase
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.

2qho__assembly_1__model_1

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

Download this curve (.dat)

2qho__assembly_1__model_1 | I(q)

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

2qho__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）16.10 Å
Rg (electron density)15.00 Å
Total Rg16.04 Å
Atom count933
Residues119
Excluded volume16809 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2qho__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2qho__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2qho__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2qho__assembly_4__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) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd2qhoa_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd2qhoc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd2qhoe_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related
Domain ID domain_idd2qhog_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.15 — beta-Grasp (ubiquitin-like)
Superfamily Superfamily superfamilyd.15.1 — Ubiquitin-like
Family Family familyd.15.1.1 — Ubiquitin-related

CATH v4.4 (8 domains)

Domain ID domain_id2qhoA00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2qhoB00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2qhoC00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2qhoD00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2qhoE00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2qhoF00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
Domain ID domain_id2qhoG00
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology20 — Ubiquitin-like (UB roll)
Homologous superfamily homologous superfamily90 — Phosphatidylinositol 3-kinase Catalytic Subunit; Chain A, domain 1
Domain ID domain_id2qhoH00
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily10 — Ubiquitin-associated (UBA) domain
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7. Citations (1)