4fx3

Crystal Structure of the CDK2/Cyclin A complex with oxindole inhibitor

Method: X-RAY DIFFRACTION Dmax: 116.2 Å Quality: REASONABLE

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

Cyclin-dependent kinase 2

Homo sapiens

UniProt P24941

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–298 Not recorded Cyclin-A2 × 1 (P20248) 60K (3Z)-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxylic acid × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293.15 K;22% polyacrylic acid 5100, 0.1M HEPES, 0.02M MgCl2, vapor diffusion, sitting drop, temperature 293.15K, pH 7.5, VAPOR DIFFUSION, SITTING DROP Resolution 2.75 Å R-free 0.240
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–298 Not recorded Cyclin-A2 × 1 (P20248) 60K (3Z)-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxylic acid × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293.15 K;22% polyacrylic acid 5100, 0.1M HEPES, 0.02M MgCl2, vapor diffusion, sitting drop, temperature 293.15K, pH 7.5, VAPOR DIFFUSION, SITTING DROP Resolution 2.75 Å R-free 0.240

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

518 other PDB entries and 663 assemblies. Open the comparison page and filter oligomeric states

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 Author chain C; PDBConstruct 1–298; UniProt 1–298

Cyclin-A2

Homo sapiens

UniProt P20248

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 175–432 Fragment:UNP RESIDUES 175-432 Cyclin-dependent kinase 2 × 1 (P24941) 60K (3Z)-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxylic acid × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293.15 K;22% polyacrylic acid 5100, 0.1M HEPES, 0.02M MgCl2, vapor diffusion, sitting drop, temperature 293.15K, pH 7.5, VAPOR DIFFUSION, SITTING DROP Resolution 2.75 Å R-free 0.240
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain D; UniProt 175–432 Fragment:UNP RESIDUES 175-432 Cyclin-dependent kinase 2 × 1 (P24941) 60K (3Z)-2-oxo-3-[2-(4-sulfamoylphenyl)hydrazinylidene]-2,3-dihydro-1H-indole-5-carboxylic acid × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7.5;293.15 K;22% polyacrylic acid 5100, 0.1M HEPES, 0.02M MgCl2, vapor diffusion, sitting drop, temperature 293.15K, pH 7.5, VAPOR DIFFUSION, SITTING DROP Resolution 2.75 Å R-free 0.240

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

113 other PDB entries and 211 assemblies. Open the comparison page and filter oligomeric states

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.

SAXS scattering curve SAXS Profile

SAXS profile for 4fx3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4fx3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4fx3
Deposition date deposition_date2012-07-02
Structure title titleCrystal Structure of the CDK2/Cyclin A complex with oxindole inhibitor
Keywords keywordsCOMPLEX (TRANSFERASE-CYCLIN), transferase-transferase inhibitor complex; transferase/transferase inhibitor
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier35.48
Radius of gyration Rg (electron density) rg_electron34.76
Forward intensity I(0) i0221894000.00
Molecular weight molecular_weight126360.0 kDa
Excluded volume excluded_volume160590 ų
Envelope volume envelope_volume200090 ų
Hydration-shell volume shell_volume47310 ų
Envelope diameter envelope_diameter121.9
Shell Rg shell_rg42.04
Envelope Rg envelope_rg34.36
Shape Rg shape_rg34.80
Total Rg total_rg35.14
Total atoms total_atoms8933
Residues n_residues1111
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax116.2
Rg (real space) rg_real35.43
Rg uncertainty (real space) rg_real_error0.89
I(0) (real space) i0_real2.2190e+08
I(0) uncertainty (real space) i0_real_error3.7400e+06
Rg (reciprocal space) rg_reciprocal35.46
I(0) (reciprocal space) i0_reciprocal221900000.0000
Solution quality estimate total_estimate0.7000
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary46.5
Skewness Skewness skewness0.278
Kurtosis Kurtosis kurtosis-0.373
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha104100000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.898; Stabil: 1.000; Sysdev: 0.186; Positv: 1.000; Valcen: 0.998; Smooth: 0.844

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (6 domains)

Domain ID domain_idd4fx3a_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4fx3b1
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4fx3b2
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4fx3c_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit
Domain ID domain_idd4fx3d1
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin
Domain ID domain_idd4fx3d2
Class classa — All alpha proteins
Fold Fold folda.74 — Cyclin-like
Superfamily Superfamily superfamilya.74.1 — Cyclin-like
Family Family familya.74.1.1 — Cyclin

CATH v4.4 (8 domains)

Domain ID domain_id4fx3A01
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_id4fx3A02
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_id4fx3B01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4fx3B02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4fx3C01
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_id4fx3C02
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_id4fx3D01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id4fx3D02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like

8. Citations (1)

9. Files and Curves (10)