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7k5j

Structure of an E1-E2-ubiquitin thioester mimetic

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

Ubiquitin

Triticum aestivum

UniProt P69326

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） Consistent with protein count
7 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 3 Ubiquitin-activating enzyme E1 1 × 1 （P22515） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 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
7k5j 7k5j 7k5j 7k5j 7k5j 7k5j 7k5j 7k5j 7sol 7sol

10 assemblies

View Construct and Data Evidence
UniProt name UBIQ_WHEAT
Isoform —
PDB entities 1
Chains and sequence ranges Author chain M； PDBConstruct 8–83； UniProt 1–76 Author chain N； PDBConstruct 8–83； UniProt 1–76 Author chain O； PDBConstruct 8–83； UniProt 1–76 Author chain P； PDBConstruct 8–83； UniProt 1–76 Author chain Q； PDBConstruct 8–83； UniProt 1–76 Author chain R； PDBConstruct 8–83； UniProt 1–76 Author chain W； PDBConstruct 8–83； UniProt 1–76 Author chain X； PDBConstruct 8–83； UniProt 1–76

Ubiquitin-activating enzyme E1 1

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P22515

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） Consistent with protein count
7 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-conjugating enzyme E2-34 kDa × 1 （P14682） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
7zh9

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
3cmm 3cmm 4nnj 5l6h 5l6h 5l6i 5l6i 5l6j 5l6j 5tr4 5tr4 6nya

29 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBA1_YEAST
Isoform —
PDB entities 2
Chains and sequence ranges Author chain A； PDBConstruct 4–1017； UniProt 11–1024 Author chain C； PDBConstruct 4–1017； UniProt 11–1024 Author chain D； PDBConstruct 4–1017； UniProt 11–1024 Author chain G； PDBConstruct 4–1017； UniProt 11–1024 Author chain I； PDBConstruct 4–1017； UniProt 11–1024 Author chain K； PDBConstruct 4–1017； UniProt 11–1024 Author chain S； PDBConstruct 4–1017； UniProt 11–1024 Author chain U； PDBConstruct 4–1017； UniProt 11–1024

Ubiquitin-conjugating enzyme E2-34 kDa

Saccharomyces cerevisiae (strain ATCC 204508 / S288c)

UniProt P14682

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） Consistent with protein count
7 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count
8 Protein heterocomplex Heteromer Protein 3 Ubiquitin × 1 （P69326） Ubiquitin-activating enzyme E1 1 × 1 （P22515） ADENOSINE MONOPHOSPHATE × 1 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6nyd

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6nya 6nya 6zhu 6zhu 6zhu 6zhu 7k5j 7k5j 7k5j 7k5j 7k5j 7k5j

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBC3_YEAST
Isoform —
PDB entities 3
Chains and sequence ranges Author chain B； PDBConstruct 5–197； UniProt 3–195 Author chain E； PDBConstruct 5–197； UniProt 3–195 Author chain F； PDBConstruct 5–197； UniProt 3–195 Author chain H； PDBConstruct 5–197； UniProt 3–195 Author chain J； PDBConstruct 5–197； UniProt 3–195 Author chain L； PDBConstruct 5–197； UniProt 3–195 Author chain T； PDBConstruct 5–197； UniProt 3–195 Author chain V； PDBConstruct 5–197； UniProt 3–195

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_id7k5j
Deposition date deposition_date2020-09-16
Structure title titleStructure of an E1-E2-ubiquitin thioester mimetic
Keywords keywords;CONFORMATIONAL CHANGE, ADENYLATION, THIOESTER TRANSFER, TRANSTHIOESTERIFICATION, ATP-BINDING, UBIQUITIN E2-BINDING, UBIQUITINATION, SIGNALING PROTEIN ;; SIGNALING 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.

7k5j__assembly_6__model_1

Assembly 6 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

7k5j__assembly_6__model_1 | I(q)

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

7k5j__assembly_6__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）35.79 Å
Rg (electron density)34.79 Å
Total Rg35.38 Å
Atom count9490
Residues1192
Excluded volume169200 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 7k5j__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 7k5j__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 7k5j__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 7k5j__assembly_4__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 7k5j__assembly_5__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 7k5j__assembly_6__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
7 1 7k5j__assembly_7__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
8 1 7k5j__assembly_8__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 24 domains

CATH v4.4 (24 domains)

Domain ID domain_id7k5jA01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jA02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jC01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jC02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jD01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jD02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jG01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jG02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jI01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jI02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jK01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jK02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jM01
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_id7k5jN01
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_id7k5jO01
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_id7k5jP01
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_id7k5jQ01
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_id7k5jR01
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_id7k5jS01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jS02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jU01
Class class2 — Mainly Beta
Architecture architecture40 — Beta Barrel
Topology topology30 — Elongation Factor Tu (Ef-tu); domain 3
Homologous superfamily homologous superfamily180 — Ubiquitin-activating enzyme E1, FCCH domain
Domain ID domain_id7k5jU02
Class class3 — Alpha Beta
Architecture architecture10 — Roll
Topology topology290 — Structural Genomics Hypothetical 15.5 Kd Protein In mrcA-pckA Intergenic Region; Chain A
Homologous superfamily homologous superfamily60 — Ubiquitin-activating enzyme E1, UFD domain
Domain ID domain_id7k5jW01
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_id7k5jX01
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
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7. Citations (1)