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8dey

Ternary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709

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

Protein cereblon

Homo sapiens

UniProt Q96SW2

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 （Q9UKS7） ZINC ION × 3 (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA damage-binding protein 1 × 1 （Q16531） Zinc finger protein Helios × 1 （Q9UKS7） ZINC ION × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
8rq1 8rq8 8rqa 9gy3 9gy3 9odr 9odr 9odr 9odr 9ods 9ods 9ods

14 assemblies; showing the first 12

Homodimer
9gao

1 assemblies

Homotetramer

None

Other homooligomers
9cuo 9cuo

2 assemblies

Heteromeric or nucleic-acid complex
10ay 11mr 4m91 4tz4 5fqd 5fqd 5hxb 5hxb 5v3o 6bn7 6bn8 6bn9

125 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name CRBN_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–373； UniProt 70–442 Author chain D； PDBConstruct 1–373； UniProt 70–442

DNA damage-binding protein 1

Homo sapiens

UniProt Q16531

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 （Q9UKS7） ZINC ION × 3 (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） Zinc finger protein Helios × 1 （Q9UKS7） ZINC ION × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3e0c 8zsw 9bbe 9bbg 9bbh 9bbi 9ejq 9zxm 9zxn

9 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
10ay 2hye 3ei1 3ei2 3ei3 3ei4 3ei4 3ei4 3i7h 3i7k 3i7l 3i7n

282 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DDB1_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain B； PDBConstruct 1–395； UniProt 1–395 Author chain B； PDBConstruct 402–836； UniProt 706–1140 Author chain E； PDBConstruct 1–395； UniProt 1–395 Author chain E； PDBConstruct 402–836； UniProt 706–1140

Zinc finger protein Helios

Homo sapiens

UniProt Q9UKS7

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） DNA damage-binding protein 1 × 1 （Q16531） ZINC ION × 3 (3S)-3-[5-(1-benzylpiperidin-4-yl)-1-oxo-1,3-dihydro-2H-isoindol-2-yl]piperidine-2,6-dione × 1 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 Protein cereblon × 1 （Q96SW2） DNA damage-binding protein 1 × 1 （Q16531） ZINC ION × 3 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
7lps 7lps 7lps 7lps 8dey 8dey 9dom 9dom 9dom 9dom 9o91 9o91

23 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name IKZF2_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 2–57； UniProt 137–192 Author chain F； PDBConstruct 2–57； UniProt 137–192

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_id8dey
Deposition date deposition_date2022-06-21
Structure title titleTernary complex structure of Cereblon-DDB1 bound to IKZF2(ZF2,3) and the molecular glue DKY709
Keywords keywordsE3 ligase, molecular glue, complex, LIGASE; 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.

8dey__assembly_1__model_1

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

Download this curve (.dat)

8dey__assembly_1__model_1 | I(q)

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

8dey__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）35.34 Å
Rg (electron density)34.56 Å
Total Rg35.13 Å
Atom count9701
Residues1230
Excluded volume173270 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 8dey__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 8dey__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 (5)

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6. Fold Classification (SCOP + CATH) 10 domains

CATH v4.4 (10 domains)

Domain ID domain_id8deyA01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily40 — LON domain-like
Domain ID domain_id8deyA02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily20 — Peptide methionine sulfoxide reductase.
Domain ID domain_id8deyB01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8deyB02
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8deyB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily910 —
Domain ID domain_id8deyD01
Class class2 — Mainly Beta
Architecture architecture30 — Roll
Topology topology130 — Archaeosine Trna-guanine Transglycosylase; Chain: A, domain 4
Homologous superfamily homologous superfamily40 — LON domain-like
Domain ID domain_id8deyD02
Class class2 — Mainly Beta
Architecture architecture170 — Beta Complex
Topology topology150 — Metal Binding Protein, Guanine Nucleotide Exchange Factor; Chain A
Homologous superfamily homologous superfamily20 — Peptide methionine sulfoxide reductase.
Domain ID domain_id8deyE01
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8deyE02
Class class2 — Mainly Beta
Architecture architecture130 — 7 Propeller
Topology topology10 — Methylamine Dehydrogenase; Chain H
Homologous superfamily homologous superfamily10 — YVTN repeat-like/Quinoprotein amine dehydrogenase
Domain ID domain_id8deyE03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily910 —
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7. Citations (1)