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5gg4

Crystal structure of USP7 with RNF169 peptide

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

Ubiquitin carboxyl-terminal hydrolase 7

Homo sapiens

UniProt Q93009

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Peptide from E3 ubiquitin-protein ligase RNF169 × 2 （Q8NCN4） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Peptide from E3 ubiquitin-protein ligase RNF169 × 2 （Q8NCN4） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1nb8 1nb8 1nbf 1yze 1yze 1yze 2f1w 2f1z 2f1z 2kvr 2ylm 4m5w

73 assemblies; showing the first 12

Homodimer
5vs6 5vsb 6f5h 6m1k 7xhh 9szo

6 assemblies

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
12zj 12zj 12zj 1nbf 1nbf 1yy6 2f1x 2f1x 2f1y 2foj 2foo 2fop

67 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBP7_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–334； UniProt 560–890 Author chain B； PDBConstruct 4–334； UniProt 560–890 Author chain C； PDBConstruct 4–334； UniProt 560–890 Author chain D； PDBConstruct 4–334； UniProt 560–890

Peptide from E3 ubiquitin-protein ligase RNF169

OrganismNot specified

UniProt Q8NCN4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 4 Ubiquitin carboxyl-terminal hydrolase 7 × 2 （Q93009） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 4 Ubiquitin carboxyl-terminal hydrolase 7 × 2 （Q93009） 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
5gg4 5gg4 5vey

3 assemblies

View Construct and Data Evidence
UniProt name RN169_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–13； UniProt 620–632 Author chain F； PDBConstruct 1–13； UniProt 620–632 Author chain G； PDBConstruct 1–13； UniProt 620–632 Author chain H； PDBConstruct 1–13； UniProt 620–632

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_id5gg4
Deposition date deposition_date2016-06-15
Structure title titleCrystal structure of USP7 with RNF169 peptide
Keywords keywordsHYDROLASE/LIGASE, HYDROLASE-LIGASE complex; HYDROLASE/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.

5gg4__assembly_1__model_1

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

Download this curve (.dat)

5gg4__assembly_1__model_1 | I(q)

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

5gg4__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）29.39 Å
Rg (electron density)28.58 Å
Total Rg29.33 Å
Atom count4954
Residues650
Excluded volume87574 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5gg4__assembly_1__model_1 tetrameric （4） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5gg4__assembly_2__model_1 tetrameric （4） 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 (2)

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6. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id5gg4A01
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_id5gg4A02
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_id5gg4B01
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_id5gg4B02
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_id5gg4C02
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_id5gg4D02
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)