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6c16

Ubiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex.

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

S-phase kinase-associated protein 1

Homo sapiens

UniProt P63208

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Lysine-specific demethylase 2A × 1 （Q9Y2K7） Polyubiquitin-B × 1 （P0CG47） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Lysine-specific demethylase 2A × 1 （Q9Y2K7） Polyubiquitin-B × 1 （P0CG47） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
5xyl

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1fqv 1fqv 1fqv 1fqv 1fqv 1fqv 1fqv 1fqv 1fs1 1fs2 1ldk 1ldk

97 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name SKP1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–165； UniProt 1–163 Author chain B； PDBConstruct 3–165； UniProt 1–163

Lysine-specific demethylase 2A

Homo sapiens

UniProt Q9Y2K7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-B × 1 （P0CG47） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 S-phase kinase-associated protein 1 × 1 （P63208） Polyubiquitin-B × 1 （P0CG47） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2yu1 2yu2 4bbq 4bbq

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6byh 6byh 6byh 6c16 6c16 7uv9

6 assemblies

View Construct and Data Evidence
UniProt name KDM2A_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain C； PDBConstruct 3–47； UniProt 888–932 Author chain F； PDBConstruct 3–47； UniProt 888–932

Polyubiquitin-B

Homo sapiens

UniProt P0CG47

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 S-phase kinase-associated protein 1 × 1 （P63208） Lysine-specific demethylase 2A × 1 （Q9Y2K7） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 S-phase kinase-associated protein 1 × 1 （P63208） Lysine-specific demethylase 2A × 1 （Q9Y2K7） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
2msg 3ons 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4wzp 4xof 5dk8

32 assemblies; showing the first 12

Homodimer
4zpz 5emz 5emz 5emz 5gob 5goc 5god 5gog 5goh 5goi 5goj 5khy

25 assemblies; showing the first 12

Homotetramer
5go8 5xdp

2 assemblies

Other homooligomers
3zlz 3zlz 3zlz 5go7 5gok 6oq1 6oq1 6oq2 7cap

9 assemblies

Heteromeric or nucleic-acid complex
2mbb 2mro 2n13 2y5b 2y5b 3o65 3o65 3o65 3o65 3o65 3o65 3oj3

362 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name UBB_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain D； PDBConstruct 4–86； UniProt 77–152 Author chain H； PDBConstruct 4–86； UniProt 77–152

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_id6c16
Deposition date deposition_date2018-01-04
Structure title titleUbiquitin variant (UbV.Fbl10.1) bound to a human Skp1-Fbl11 fragment complex.
Keywords keywordsUbiquitination, 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.

6c16__assembly_1__model_1

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

Download this curve (.dat)

6c16__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

6c16__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）21.22 Å
Rg (electron density)20.10 Å
Total Rg20.92 Å
Atom count1774
Residues251
Excluded volume31234 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6c16__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6c16__assembly_2__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 (3)

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id6c16A00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
Domain ID domain_id6c16B00
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology710 — Potassium Channel Kv1.1; Chain A
Homologous superfamily homologous superfamily10 — Potassium Channel Kv1.1; Chain A
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7. Citations (1)