9etb

CDK2-cyclin A in complex with FragLite 2

Method: X-RAY DIFFRACTION Dmax: 114.9 Å Quality: GOOD

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

Cyclin-A2

Bos taurus

UniProt P30274

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 D; UniProt 170–430 Not recorded Cyclin-dependent kinase 2 × 1 (P24941) PYZ 4-IODOPYRAZOLE × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;277 K;Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0 Resolution 2.76 Å R-free 0.228
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 170–430 Not recorded Cyclin-dependent kinase 2 × 1 (P24941) PYZ 4-IODOPYRAZOLE × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;277 K;Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0 Resolution 2.76 Å R-free 0.228

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.

44 other PDB entries and 86 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CCNA2_BOVIN
Isoform
PDB entities 1
Chains and sequence ranges Author chain B; PDBConstruct 2–262; UniProt 170–430 Author chain D; PDBConstruct 2–262; UniProt 170–430

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 C; UniProt 1–298 Non-standard monomer:Yes (specific site not provided by mmCIF) Cyclin-A2 × 1 (P30274) PYZ 4-IODOPYRAZOLE × 4 EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;277 K;Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0 Resolution 2.76 Å R-free 0.228
2 Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–298 Non-standard monomer:Yes (specific site not provided by mmCIF) Cyclin-A2 × 1 (P30274) PYZ 4-IODOPYRAZOLE × 8 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 7;277 K;Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0 Resolution 2.76 Å R-free 0.228

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 2
Chains and sequence ranges Author chain A; PDBConstruct 5–302; UniProt 1–298 Author chain C; PDBConstruct 5–302; UniProt 1–298

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 9etb

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9etb
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9etb
Deposition date deposition_date2024-03-26
Structure title titleCDK2-cyclin A in complex with FragLite 2
Keywords keywordscyclin-dependent kinase, FragLite, CDK2, cyclin A, Fragment, CELL CYCLE; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier34.66
Radius of gyration Rg (electron density) rg_electron33.93
Forward intensity I(0) i0246599000.00
Molecular weight molecular_weight129860.0 kDa
Excluded volume excluded_volume163440 ų
Envelope volume envelope_volume201560 ų
Hydration-shell volume shell_volume48386 ų
Envelope diameter envelope_diameter121.0
Shell Rg shell_rg41.65
Envelope Rg envelope_rg33.65
Shape Rg shape_rg33.99
Total Rg total_rg34.30
Total atoms total_atoms9070
Residues n_residues1114
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 dmax114.9
Rg (real space) rg_real34.58
Rg uncertainty (real space) rg_real_error0.78
I(0) (real space) i0_real2.4660e+08
I(0) uncertainty (real space) i0_real_error3.7290e+06
Rg (reciprocal space) rg_reciprocal34.63
I(0) (reciprocal space) i0_reciprocal246600000.0000
Solution quality estimate total_estimate0.8842
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary47.5
Skewness Skewness skewness0.249
Kurtosis Kurtosis kurtosis-0.333
Angular range angular_range— – 0.2300 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha111400000.0000
Real-space data points n_real_points47
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.859; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

8. Citations (1)

9. Files and Curves (10)