SAXSdb — 8d7m

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

Casein kinase I isoform delta

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	Period circadian protein homolog 2 peptide × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Period circadian protein homolog 2 peptide × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KC1D_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 8–301； UniProt 1–294 Author chain B； PDBConstruct 8–301； UniProt 1–294

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_id	8d7m
Deposition date deposition_date	2022-06-07
Structure title title	Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide
Keywords keywords	Transferase, CIRCADIAN CLOCK PROTEIN, Kinase, complex, TRANSFERASE-CIRCADIAN CLOCK PROTEIN complex; TRANSFERASE/CIRCADIAN CLOCK PROTEIN
Experimental Method method	X-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.

8d7m__assembly_1__model_1

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

Download this curve (.dat)

8d7m__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8d7m__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	20.53 Å
Rg (electron density)	19.40 Å
Total Rg	20.36 Å
Atom count	2410
Residues	293
Excluded volume	43032 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8d7m__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`8d7m__assembly_2__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 (3)

Entity 1 Entity 1 polymer

Description description	Casein kinase I isoform delta
Molecular weight formula_weight	34954.3 kDa
EC 编号 ec_number	2.7.11.1,2.7.11.26
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	5074

GAMDPEFMELRVGNRYRLGRKIGSGSFGDIYLGTDIAAGEEVAIKLECVKTKHPQLHIESKIYKMMQGGVGIPTIRWCGAEGDYNVMVMELLGPSLEDLFNFCSRKFSLKTVLLLADQMISRIEYIHSKNFIHRDVKPDNFLMGLGKKGNLVYIIDFGLAKKYRDARTHQHIPYRENKNLTGTARYASINTHLGIEQSRRDDLESLGYVLMYFNLGSLPWQGLKAATKRQKYERISEKKMSTPIEVLCKGYPSEFATYLNFCRSLRFDDKPDYSYLRQLFRNLFHRQGFSYDYVFDWNMLK

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Period circadian protein homolog 2 peptide
Molecular weight formula_weight	1123.0 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

GKAESVASLT

Entity 3 Entity 3 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	254

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id	8d7mA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	8d7mA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

Domain ID domain_id	8d7mB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily	20 — Phosphorylase Kinase; domain 1

Domain ID domain_id	8d7mB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily	10 — Transferase(Phosphotransferase) domain 1

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Unit-cell length a length_a	55.700 Å
Unit-cell length b length_b	135.970 Å
Unit-cell length c length_c	91.140 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	94.33 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.250 Å
Low-resolution limit resolution_low	46.155 Å
R factor r_factor	0.1835
R_work r_work	0.1807
R_free r_free	0.2333

Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide

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

Casein kinase I isoform delta

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8d7m__assembly_1__model_1

8d7m__assembly_1__model_1 | I(q)

8d7m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)

Human Casein kinase 1 delta in complex with phosphorylated human PERIOD2 FASP peptide

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

Casein kinase I isoform delta

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

8d7m__assembly_1__model_1

8d7m__assembly_1__model_1 | I(q)

8d7m__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 water

6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

7. Citations (1)