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5fqd

Structural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase

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

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） CASEIN KINASE I ISOFORM ALPHA × 1 （P48729） ZINC ION × 1 S-Lenalidomide × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 PROTEIN CEREBLON × 1 （Q96SW2） CASEIN KINASE I ISOFORM ALPHA × 1 （P48729） ZINC ION × 1 S-Lenalidomide × 1 water × 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 1
Chains and sequence ranges Author chain A； PDBConstruct 21–415； UniProt 1–395 Author chain A； PDBConstruct 425–856； UniProt 709–1140 Author chain D； PDBConstruct 21–415； UniProt 1–395 Author chain D； PDBConstruct 425–856； UniProt 709–1140

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） CASEIN KINASE I ISOFORM ALPHA × 1 （P48729） ZINC ION × 1 S-Lenalidomide × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） CASEIN KINASE I ISOFORM ALPHA × 1 （P48729） ZINC ION × 1 S-Lenalidomide × 1 water × 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 2
Chains and sequence ranges Author chain B； PDBConstruct 25–426； UniProt 41–442 Author chain E； PDBConstruct 25–426； UniProt 41–442

CASEIN KINASE I ISOFORM ALPHA

HOMO SAPIENS

UniProt P48729

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） PROTEIN CEREBLON × 1 （Q96SW2） ZINC ION × 1 S-Lenalidomide × 1 water × 3 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 3 DNA DAMAGE-BINDING PROTEIN 1 × 1 （Q16531） PROTEIN CEREBLON × 1 （Q96SW2） ZINC ION × 1 S-Lenalidomide × 1 water × 3 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
6gzd

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
5fqd 5fqd 7wtt 8g66 8g66 9oty

6 assemblies

View Construct and Data Evidence
UniProt name KC1A_HUMAN
Isoform —
PDB entities 3
Chains and sequence ranges Author chain C； PDBConstruct 5–341； UniProt 1–337 Author chain F； PDBConstruct 5–341； UniProt 1–337

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_id5fqd
Deposition date deposition_date2015-12-09
Structure title titleStructural basis of Lenalidomide induced CK1a degradation by the crl4crbn ubiquitin ligase
Keywords keywordsLIGASE, DNA BINDING; 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.

5fqd__assembly_1__model_1

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

Download this curve (.dat)

5fqd__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.

5fqd__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）43.24 Å
Rg (electron density)43.58 Å
Total Rg43.66 Å
Atom count11639
Residues1464
Excluded volume207930 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5fqd__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 5fqd__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 (6)

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6. Fold Classification (SCOP + CATH) 18 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd5fqdc_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd5fqdf_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (16 domains)

Domain ID domain_id5fqdA01
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_id5fqdA02
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_id5fqdA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily910 —
Domain ID domain_id5fqdB01
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_id5fqdB02
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_id5fqdB03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1480 —
Domain ID domain_id5fqdC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5fqdC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
Domain ID domain_id5fqdD01
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_id5fqdD02
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_id5fqdD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily910 —
Domain ID domain_id5fqdE01
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_id5fqdE02
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_id5fqdE03
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology58 — Methane Monooxygenase Hydroxylase; Chain G, domain 1
Homologous superfamily homologous superfamily1480 —
Domain ID domain_id5fqdF01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id5fqdF02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
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7. Citations (1)