2cci

Crystal structure of phospho-CDK2 Cyclin A in complex with a peptide containing both the substrate and recruitment sites of CDC6

Method: X-RAY DIFFRACTION Dmax: 138.0 Å Quality: GOOD

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain A; UniProt 1–298 Non-standard monomer:Yes (specific site not provided by mmCIF) Cyclin-A2 × 1 (P20248) Cell division control protein 6 homolog × 1 (Q99741) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.6;10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5 Resolution 2.70 Å R-free 0.321
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain C; UniProt 1–298 Non-standard monomer:Yes (specific site not provided by mmCIF) Cyclin-A2 × 1 (P20248) Cell division control protein 6 homolog × 1 (Q99741) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.6;10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5 Resolution 2.70 Å R-free 0.321

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 2–299; UniProt 1–298 Author chain C; PDBConstruct 2–299; 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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain B; UniProt 175–432 Fragment:RESIDUES 175-432 Cyclin-dependent kinase 2 × 1 (P24941) Cell division control protein 6 homolog × 1 (Q99741) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.6;10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5 Resolution 2.70 Å R-free 0.321
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain D; UniProt 175–432 Fragment:RESIDUES 175-432 Cyclin-dependent kinase 2 × 1 (P24941) Cell division control protein 6 homolog × 1 (Q99741) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.6;10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5 Resolution 2.70 Å R-free 0.321

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

Cell division control protein 6 homolog

OrganismNot specified

UniProt Q99741

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 × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain F; UniProt 71–100 Fragment:RESIDUES 71-100 Mutation:YES Cyclin-dependent kinase 2 × 1 (P24941) Cyclin-A2 × 1 (P20248) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.6;10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5 Resolution 2.70 Å R-free 0.321
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric(3) Consistent with protein copy count Chain I; UniProt 71–100 Fragment:RESIDUES 71-100 Mutation:YES Cyclin-dependent kinase 2 × 1 (P24941) Cyclin-A2 × 1 (P20248) ATP ADENOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:pH 5.6;10-17% (V/V) PEG MONOMETHYLETHER 5000, 0.2 M AMMONIUM SULPHATE AND 0.1 M MES PH 5.0-6.5 Resolution 2.70 Å R-free 0.321

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.

5 other PDB entries and 8 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name CDC6_HUMAN
Isoform
PDB entities 3
Chains and sequence ranges Author chain F; PDBConstruct 1–30; UniProt 71–100 Author chain I; PDBConstruct 1–30; UniProt 71–100

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 2cci

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2cci
Download Download

2. Structure Basics 2. Structure Basics

Entry ID entry_id2cci
Deposition date deposition_date2006-01-16
Structure title titleCrystal structure of phospho-CDK2 Cyclin A in complex with a peptide containing both the substrate and recruitment sites of CDC6
Keywords keywords;COMPLEX (TRANSFERASE-CELL DIVISION), PROTEIN KINASES, CELL CYCLE, RECRUITMENT, SUBSTRATE RECOGNITION, ATP-BINDING, CELL DIVISION, KINASE, MITOSIS, NUCLEOTIDE-BINDING, PHOSPHORYLATION, SERINE/THREONINE- PROTEIN KINASE, TRANSFERASE, CYCLIN, DNA REPLICATION, NUCLEAR PROTEIN, COMPLEX ;; CELL CYCLE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier39.54
Radius of gyration Rg (electron density) rg_electron39.73
Forward intensity I(0) i0241142000.00
Molecular weight molecular_weight131700.0 kDa
Excluded volume excluded_volume167180 ų
Envelope volume envelope_volume215920 ų
Hydration-shell volume shell_volume46812 ų
Envelope diameter envelope_diameter142.4
Shell Rg shell_rg43.32
Envelope Rg envelope_rg39.32
Shape Rg shape_rg39.72
Total Rg total_rg39.96
Total atoms total_atoms9280
Residues n_residues1141
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 dmax138.0
Rg (real space) rg_real39.88
Rg uncertainty (real space) rg_real_error1.62
I(0) (real space) i0_real2.4110e+08
I(0) uncertainty (real space) i0_real_error4.9510e+06
Rg (reciprocal space) rg_reciprocal39.67
I(0) (reciprocal space) i0_reciprocal241100000.0000
Solution quality estimate total_estimate0.8426
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary41.4
Skewness Skewness skewness0.492
Kurtosis Kurtosis kurtosis-0.333
Angular range angular_range— – 0.2000 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha57840000.0000
Real-space data points n_real_points41
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.784; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.814; Smooth: 0.785

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (6)

7. Fold Classification (SCOP + CATH) 16 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2ccia2
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_idd2ccia3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2ccib1
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_idd2ccib2
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_idd2ccic2
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_idd2ccic3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd2ccid1
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_idd2ccid2
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_id2cciA01
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_id2cciA02
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_id2cciB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id2cciB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id2cciC01
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_id2cciC02
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_id2cciD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology472 — Cyclin A; domain 1
Homologous superfamily homologous superfamily10 — Cyclin-like
Domain ID domain_id2cciD02
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)