SAXSdb — 9csk

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

G1/S-specific cyclin-D1

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	Cyclin-dependent kinase 4 × 1 （P11802） Atirmociclib × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cyclin-dependent kinase 4 × 1 （P11802） Atirmociclib × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCND1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–257； UniProt 16–271 Author chain C； PDBConstruct 2–257； UniProt 16–271

Cyclin-dependent kinase 4

Homo sapiens

UniProt P11802

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	G1/S-specific cyclin-D1 × 1 （P24385） Atirmociclib × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	G1/S-specific cyclin-D1 × 1 （P24385） Atirmociclib × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDK4_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–300； UniProt 1–303 Author chain D； PDBConstruct 1–300； UniProt 1–303

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	9csk
Deposition date deposition_date	2024-07-24
Last revision last_revision	2025-03-26
Structure title title	Crystal structure of CDK4 cyclin D1 in complex with atirmociclib
Keywords keywords	Kinase, Inhibitor, Cancer, Transferase-Inhibitor-Cell Cycle complex; Transferase/Inhibitor/Cell Cycle
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.

9csk__assembly_1__model_1

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

Download this curve (.dat)

9csk__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

9csk__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	27.60 Å
Rg (electron density)	26.77 Å
Total Rg	27.51 Å
Atom count	4088
Residues	512
Excluded volume	73348 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`9csk__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`9csk__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 (4)

Entity 1 Entity 1 polymer

Description description	G1/S-specific cyclin-D1
Molecular weight formula_weight	29276.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	8626

MAYPDANLLNDRVLRAMLKAEETCAPSVSYFKCVQKEVLPSMRKIVATWMLEVCEEQKCEEEVFPLAMNYLDRFLSLEPVKKSRLQLLGATCMFVASKMKETIPLTAEKLCIYTDNSIRPEELLQMELLLVNKLKWNLAAMTPHDFIEHFLSKMPEAEENKQIIRKHAQTFVALCATDVKFISNPPSMVAAGSVVAAVQGLNLRSPNNFLSYYRLTRFLSRVIKCDPDCLRACQEQIEALLESSLRQAQQNMDPKAA

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 2 Entity 2 polymer

Description description	Cyclin-dependent kinase 4
Molecular weight formula_weight	35539.7 kDa
EC 编号 ec_number	2.7.11.22
Mutation mutation	DELTA(43-47)EE
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

MATSRYEPVAEIGVGAYGTVYKARDPHSGHFVALKSVRVPNGEEGLPISTVREVALLRRLEAFEHPNVVRLMDVCATSRTDREIKVTLVFEHVDQDLRTYLDKAPPPGLPAETIKDLMRQFLRGLDFLHANCIVHRDLKPENILVTSGGTVKLADFGLARIYSYQMALTPVVVTLWYRAPEVLLQSTYATPVDMWSVGCIFAEMFRRKPLFCGNSEADQLGKIFDLIGLPPEDDWPRDVSLPRGAFPPRGPRPVQSVVPEMEESGAQLLLEMLTFNPHKRISAFRALQHSYLHKDEGNPELENLYFQGHHHHHH

Source Source

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Spodoptera frugiperda

Entity 3 Entity 3 non-polymer

Description description	Atirmociclib
Molecular weight formula_weight	463.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	328

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Unit-cell length a length_a	56.511 Å
Unit-cell length b length_b	64.289 Å
Unit-cell length c length_c	186.208 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	91.67 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.253 Å
Low-resolution limit resolution_low	38.930 Å
R factor r_factor	0.2262
R_work r_work	0.2239
R_free r_free	0.2701

Crystal structure of CDK4 cyclin D1 in complex with atirmociclib

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

G1/S-specific cyclin-D1

State in the Current Structure

Other States of the Same Protein in the Database

Cyclin-dependent kinase 4

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

9csk__assembly_1__model_1

9csk__assembly_1__model_1 | I(q)

9csk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)

Crystal structure of CDK4 cyclin D1 in complex with atirmociclib

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

G1/S-specific cyclin-D1

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

Cyclin-dependent kinase 4

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

9csk__assembly_1__model_1

9csk__assembly_1__model_1 | I(q)

9csk__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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 water

7. Citations (1)