SAXSdb — 8vq4

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

Cyclin-dependent kinase 2

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	G1/S-specific cyclin-E1 × 1 （P24864） ;(8R)-6-(1-benzyl-1H-pyrazole-4-carbonyl)-N-[(2S,3R)-3-(2-cyclohexylethoxy)-1-(methylamino)-1-oxobutan-2-yl]-2-[(1S)-2,2-dimethylcyclopropane-1-carbonyl]-2,6-diazaspiro[3.4]octane-8-carboxamide ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CDK2_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–298； UniProt 1–298

G1/S-specific cyclin-E1

Homo sapiens

UniProt P24864

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 2 × 1 （P24941） ;(8R)-6-(1-benzyl-1H-pyrazole-4-carbonyl)-N-[(2S,3R)-3-(2-cyclohexylethoxy)-1-(methylamino)-1-oxobutan-2-yl]-2-[(1S)-2,2-dimethylcyclopropane-1-carbonyl]-2,6-diazaspiro[3.4]octane-8-carboxamide ; × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCNE1_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–285； UniProt 96–378

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	8vq4
Deposition date deposition_date	2024-01-17
Structure title title	CDK2-CyclinE1 in complex with allosteric inhibitor I-125A.
Keywords keywords	kinase, CELL CYCLE-TRANSFERASE-INHIBITOR complex; CELL CYCLE/TRANSFERASE/INHIBITOR
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.

8vq4__assembly_1__model_1

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

Download this curve (.dat)

8vq4__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

8vq4__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.40 Å
Rg (electron density)	25.31 Å
Total Rg	26.26 Å
Atom count	4563
Residues	563
Excluded volume	82459 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`8vq4__assembly_1__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	Cyclin-dependent kinase 2
Molecular weight formula_weight	34056.5 kDa
EC 编号 ec_number	2.7.11.22
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	4789

MENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLHQDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPQNLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

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	G1/S-specific cyclin-E1
Molecular weight formula_weight	33053.5 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSIIAPSRGSPLPVLSWANREEVWKIMLNKEKTYLRDQHFLEQHPLLQPKMRAILLDWLMEVCEVYKLHRETFYLAQDFFDRYMATQENVVKTLLQLIGISSLFIAAKLEEIYPPKLHQFAYVTDGACSGDEILTMELMIMKALKWRLSPLTIVSWLNVYMQVAYLNDLHEVLLPQYPQQIFIQIAELLDLCVLDVDCLEFPYGILAASALYHFSSSELMQKVSGYQWCDIENCVKWMVPFAMVIRETGSSKLKHFRGVADEDAHNIQTHRDSLDLLDKARAKKA

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	;(8R)-6-(1-benzyl-1H-pyrazole-4-carbonyl)-N-[(2S,3R)-3-(2-cyclohexylethoxy)-1-(methylamino)-1-oxobutan-2-yl]-2-[(1S)-2,2-dimethylcyclopropane-1-carbonyl]-2,6-diazaspiro[3.4]octane-8-carboxamide ;
Molecular weight formula_weight	660.8 kDa
Source method src_method	nat
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	226

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Unit-cell length a length_a	101.374 Å
Unit-cell length b length_b	101.374 Å
Unit-cell length c length_c	151.607 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	tetragonal

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	45.230 Å
R factor r_factor	0.1930
R_work r_work	0.1915
R_free r_free	0.2186

CDK2-CyclinE1 in complex with allosteric inhibitor I-125A.

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

Cyclin-dependent kinase 2

State in the Current Structure

Other States of the Same Protein in the Database

G1/S-specific cyclin-E1

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

8vq4__assembly_1__model_1

8vq4__assembly_1__model_1 | I(q)

8vq4__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 (2)

CDK2-CyclinE1 in complex with allosteric inhibitor I-125A.

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

Cyclin-dependent kinase 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

G1/S-specific cyclin-E1

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

8vq4__assembly_1__model_1

8vq4__assembly_1__model_1 | I(q)

8vq4__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 (2)