← Back to search
6ru8

Crystal structure of Casein Kinase I delta (CK1d) in complex with triple phosphorylated p63 PAD3P peptide

Method: X-RAY DIFFRACTION
▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

Casein kinase I isoform delta

Homo sapiens

UniProt P48730

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Tumor protein 63 × 1 （Q9H3D4） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 5 SODIUM ION × 1 SULFATE ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Tumor protein 63 × 1 （Q9H3D4） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 4 SODIUM ION × 1 SULFATE ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Tumor protein 63 × 1 （Q9H3D4） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 6 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Tumor protein 63 × 1 （Q9H3D4） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 3 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
3uys 3uys 3uys 3uys 3uyt 3uyt 3uyt 3uyt 3uzp 3uzp 4hgt 4hgt

92 assemblies; showing the first 12

Homodimer
3uys 3uys 3uyt 3uyt 3uzp 4hnf 4kb8 4kb8 4kba 4kba 4kbc 4kbc

22 assemblies; showing the first 12

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
6ru6 6ru7 6ru7 6ru8 6ru8 6ru8 6ru8 8d7m 8d7m 8d7n 8d7n 8d7o

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name KC1D_HUMAN
Isoform P48730-2
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 3–296； UniProt 1–294 Author chain B； PDBConstruct 3–296； UniProt 1–294 Author chain C； PDBConstruct 3–296； UniProt 1–294 Author chain D； PDBConstruct 3–296； UniProt 1–294

Tumor protein 63

OrganismNot specified

UniProt Q9H3D4

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 Casein kinase I isoform delta × 1 （P48730） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 5 SODIUM ION × 1 SULFATE ION × 1 water × 2 Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 Casein kinase I isoform delta × 1 （P48730） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 4 SODIUM ION × 1 SULFATE ION × 2 water × 2 Consistent with protein count
3 Protein heterocomplex Heteromer Protein 2 Casein kinase I isoform delta × 1 （P48730） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 6 water × 2 Consistent with protein count
4 Protein heterocomplex Heteromer Protein 2 Casein kinase I isoform delta × 1 （P48730） ADENOSINE-5'-DIPHOSPHATE × 1 1,2-ETHANEDIOL × 3 water × 2 Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1rg6 2rmn 2y9t 2y9u

4 assemblies

Homodimer

None

Homotetramer
3zy0 3zy1 4a9z

3 assemblies

Other homooligomers

None

Heteromeric or nucleic-acid complex
2nb1 3qym 3qym 3qym 3qyn 3us0 3us1 3us2 3us2 6fgn 6ru6 6ru7

30 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name P63_HUMAN
Isoform —
PDB entities 2
Chains and sequence ranges Author chain E； PDBConstruct 1–12； UniProt 621–632 Author chain F； PDBConstruct 1–12； UniProt 621–632 Author chain G； PDBConstruct 1–12； UniProt 621–632 Author chain H； PDBConstruct 1–12； UniProt 621–632

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id6ru8
Deposition date deposition_date2019-05-27
Structure title titleCrystal structure of Casein Kinase I delta (CK1d) in complex with triple phosphorylated p63 PAD3P peptide
Keywords keywords;CK1 delta, CK1delta, CSNK1D, TP63, p63, kinase substrate complex, Structural Genomics, Structural Genomics Consortium, SGC, TRANSFERASE ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION
▼

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.

6ru8__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6ru8__assembly_4__model_1 | I(q)

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

6ru8__assembly_4__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）20.52 Å
Rg (electron density)19.48 Å
Total Rg20.45 Å
Atom count2494
Residues299
Excluded volume44383 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6ru8__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 6ru8__assembly_2__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 6ru8__assembly_3__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 6ru8__assembly_4__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (7)

▼

6. Fold Classification (SCOP + CATH) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id6ru8A01
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_id6ru8A02
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_id6ru8B01
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_id6ru8B02
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_id6ru8C01
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_id6ru8C02
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_id6ru8D01
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_id6ru8D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1
▶

7. Citations (1)