4eon

Thr 160 phosphorylated CDK2 H84S, Q85M, Q131E - human cyclin A3 complex with the inhibitor RO3306

Method: X-RAY DIFFRACTION

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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	Cyclin-A2 × 1 （P20248） (5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cyclin-A2 × 1 （P20248） (5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one × 1 MAGNESIUM ION × 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 3–300； UniProt 1–298 Author chain C； PDBConstruct 3–300； UniProt 1–298

Cyclin-A2

Homo sapiens

UniProt P20248

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） (5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	Cyclin-dependent kinase 2 × 1 （P24941） (5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one × 1 MAGNESIUM ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	CCNA2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–258； UniProt 175–432 Author chain D； PDBConstruct 1–258； UniProt 175–432

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	4eon
Deposition date deposition_date	2012-04-14
Structure title title	Thr 160 phosphorylated CDK2 H84S, Q85M, Q131E - human cyclin A3 complex with the inhibitor RO3306
Keywords keywords	protein kinase, cell cycle, PHOSPHORYLATION, TRANSFERASE-TRANSFERASE INHIBITOR complex; TRANSFERASE/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.

4eon__assembly_1__model_1

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

Download this curve (.dat)

4eon__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

4eon__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.53 Å
Rg (electron density)	25.55 Å
Total Rg	26.49 Å
Atom count	4507
Residues	556
Excluded volume	81401 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`4eon__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`4eon__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 (5)

Entity 1 Entity 1 polymer

Description description	Cyclin-dependent kinase 2
Molecular weight formula_weight	34153.6 kDa
EC 编号 ec_number	2.7.11.22
Mutation mutation	H84S, Q85M, Q131E
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	9199

GSMENFQKVEKIGEGTYGVVYKARNKLTGEVVALKKIRLDTETEGVPSTAIREISLLKELNHPNIVKLLDVIHTENKLYLVFEFLSMDLKKFMDASALTGIPLPLIKSYLFQLLQGLAFCHSHRVLHRDLKPENLLINTEGAIKLADFGLARAFGVPVRTYTHEVVTLWYRAPEILLGCKYYSTAVDIWSLGCIFAEMVTRRALFPGDSEIDQLFRIFRTLGTPDEVVWPGVTSMPDYKPSFPKWARQDFSKVVPPLDEDGRSLLSQMLHYDPNKRISAKAALAHPFFQDVTKPVPHLRL

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	Cyclin-A2
Molecular weight formula_weight	29624.3 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

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

VPDYHEDIHTYLREMEVKCKPKVGYMKKQPDITNSMRAILVDWLVEVGEEYKLQNETLHLAVNYIDRFLSSMSVLRGKLQLVGTAAMLLASKFEEIYPPEVAEFVYITDDTYTKKQVLRMEHLVLKVLTFDLAAPTVNQFLTQYFLHQQPANCKVESLAMFLGELSLIDADPYLKYLPSVIAGAAFHLALYTVTGQSWPESLIRKTGYTLESLKPCLMDLHQTYLKAPQHAQQSIREKYKNSKYHGVSLLNPPETLNL

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 3 Entity 3 non-polymer

Description description	(5E)-5-(quinolin-6-ylmethylidene)-2-[(thiophen-2-ylmethyl)amino]-1,3-thiazol-4(5H)-one
Molecular weight formula_weight	351.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	130

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6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d4eona1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d4eona2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4eonb1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4eonb2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4eonc1
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamily	d.144.1 — Protein kinase-like (PK-like)
Family Family family	d.144.1.7 — Protein kinases, catalytic subunit

Domain ID domain_id	d4eonc2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d4eond1
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

Domain ID domain_id	d4eond2
Class class	a — All alpha proteins
Fold Fold fold	a.74 — Cyclin-like
Superfamily Superfamily superfamily	a.74.1 — Cyclin-like
Family Family family	a.74.1.1 — Cyclin

CATH v4.4 (8 domains)

Domain ID domain_id	4eonA01
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	4eonA02
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	4eonB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4eonB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4eonC01
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	4eonC02
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	4eonD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

Domain ID domain_id	4eonD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily	10 — Cyclin-like

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Unit-cell length a length_a	73.626 Å
Unit-cell length b length_b	132.979 Å
Unit-cell length c length_c	176.727 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 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	29.860 Å
R factor r_factor	0.2205
R_work r_work	0.2187
R_free r_free	0.2543

Thr 160 phosphorylated CDK2 H84S, Q85M, Q131E - human cyclin A3 complex with the inhibitor RO3306

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

Cyclin-A2

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

4eon__assembly_1__model_1

4eon__assembly_1__model_1 | I(q)

4eon__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Thr 160 phosphorylated CDK2 H84S, Q85M, Q131E - human cyclin A3 complex with the inhibitor RO3306

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

Cyclin-A2

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

4eon__assembly_1__model_1

4eon__assembly_1__model_1 | I(q)

4eon__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 (5)

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 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

CATH v4.4 (8 domains)

7. Citations (1)