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2c7n

Human Rabex-5 residues 1-74 in complex with Ubiquitin

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

RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1

HOMO SAPIENS

UniProt Q53FG0

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） ZINC ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 UBIQUITIN × 1 （P62990） ZINC ION × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 UBIQUITIN × 1 （P62990） ZINC ION × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 UBIQUITIN × 1 （P62990） ZINC ION × 1 water × 2 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 UBIQUITIN × 1 （P62990） ZINC ION × 1 water × 2 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 UBIQUITIN × 1 （P62990） ZINC ION × 1 water × 2 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
2c7m 2c7n 2c7n 2c7n 2c7n 2c7n 2c7n

7 assemblies

View Construct and Data Evidence
UniProt name Q53FG0_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–74； UniProt 1–74 Author chain C； PDBConstruct 1–74； UniProt 1–74 Author chain E； PDBConstruct 1–74； UniProt 1–74 Author chain G； PDBConstruct 1–74； UniProt 1–74 Author chain I； PDBConstruct 1–74； UniProt 1–74 Author chain K； PDBConstruct 1–74； UniProt 1–74

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 RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） ZINC ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） ZINC ION × 1 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） ZINC ION × 1 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） ZINC ION × 1 water × 2 Consistent with protein count
5 Protein heterocomplex Heteromer Protein 2 RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） ZINC ION × 1 water × 2 Consistent with protein count
6 Protein heterocomplex Heteromer Protein 2 RAB GUANINE NUCLEOTIDE EXCHANGE FACTOR 1 × 1 （Q53FG0） ZINC ION × 1 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 2
Chains and sequence ranges Author chain B； PDBConstruct 1–76； UniProt 1–76 Author chain D； PDBConstruct 1–76； UniProt 1–76 Author chain F； PDBConstruct 1–76； UniProt 1–76 Author chain H； PDBConstruct 1–76； UniProt 1–76 Author chain J； PDBConstruct 1–76； UniProt 1–76 Author chain L； PDBConstruct 1–76； UniProt 1–76

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_id2c7n
Deposition date deposition_date2005-11-25
Structure title titleHuman Rabex-5 residues 1-74 in complex with Ubiquitin
Keywords keywordsPROTEIN-BINDING, UBIQUITIN BINDING DOMAIN, ENDOCYTOSIS, NUCLEAR PROTEIN, POLYPROTEIN, UBIQUITIN COMPLEX, PROTEIN BINDING; PROTEIN BINDING
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.

2c7n__assembly_1__model_1

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

Download this curve (.dat)

2c7n__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.

2c7n__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）18.35 Å
Rg (electron density)17.46 Å
Total Rg18.40 Å
Atom count1048
Residues130
Excluded volume18579 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2c7n__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2c7n__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2c7n__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2c7n__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
5 1 2c7n__assembly_5__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
6 1 2c7n__assembly_6__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 (4)

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6. Fold Classification (SCOP + CATH) 22 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd2c7na1
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.15 — A20-like zinc finger
Domain ID domain_idd2c7nb1
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_idd2c7nc1
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.15 — A20-like zinc finger
Domain ID domain_idd2c7nd1
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_idd2c7nf1
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_idd2c7ng1
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.15 — A20-like zinc finger
Domain ID domain_idd2c7nh1
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_idd2c7ni1
Class classg — Small proteins
Fold Fold foldg.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamilyg.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family familyg.39.1.15 — A20-like zinc finger
Domain ID domain_idd2c7nj1
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_idd2c7nl1
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 (12 domains)

Domain ID domain_id2c7nA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4770 —
Domain ID domain_id2c7nB00
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_id2c7nC01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4770 —
Domain ID domain_id2c7nD00
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_id2c7nE01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4770 —
Domain ID domain_id2c7nF00
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_id2c7nG01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4770 —
Domain ID domain_id2c7nH00
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_id2c7nI01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4770 —
Domain ID domain_id2c7nJ00
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_id2c7nK01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily4770 —
Domain ID domain_id2c7nL00
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)