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- PDB-3ddp: Structure of phosphorylated Thr160 CDK2/cyclin A in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3ddp
TitleStructure of phosphorylated Thr160 CDK2/cyclin A in complex with the inhibitor CR8
Components
  • Cell division protein kinase 2
  • Cyclin-A2
KeywordsTRANSFERASE/CELL CYCLE / Ser/Thr protein kinase / phosphorylation / cell cycle / ATP-binding / Cell division / Mitosis / Nucleotide-binding / Phosphoprotein / Polymorphism / Serine/threonine-protein kinase / Cyclin / Cytoplasm / Nucleus / TRANSFERASE-CELL CYCLE COMPLEX
Function / homology
Function and homology information


cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity / G2 Phase / Y chromosome ...cell cycle G1/S phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / cyclin-dependent protein kinase activity / G2 Phase / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation / p53-Dependent G1 DNA Damage Response / X chromosome / PTK6 Regulates Cell Cycle / regulation of anaphase-promoting complex-dependent catabolic process / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / microtubule organizing center / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / regulation of DNA replication / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / male germ cell nucleus / positive regulation of DNA replication / meiotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / peptidyl-serine phosphorylation / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / DNA replication / endosome / protein phosphorylation / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / centrosome / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Similarity search - Function
Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain / Serine/Threonine protein kinases, catalytic domain / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Protein kinase domain profile. / Protein kinase domain / Protein kinase-like domain superfamily / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Chem-RC8 / Cyclin-dependent kinase 2 / Cyclin-A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsEchalier, A. / Endicott, J.A.
CitationJournal: Oncogene / Year: 2008
Title: CR8, a potent and selective, roscovitine-derived inhibitor of cyclin-dependent kinases.
Authors: Bettayeb, K. / Oumata, N. / Echalier, A. / Ferandin, Y. / Endicott, J.A. / Galons, H. / Meijer, L.
History
DepositionJun 6, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jul 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cell division protein kinase 2
B: Cyclin-A2
C: Cell division protein kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8456
Polymers129,9824
Non-polymers8632
Water2,414134
1
C: Cell division protein kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4233
Polymers64,9912
Non-polymers4321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3660 Å2
ΔGint-16 kcal/mol
Surface area24160 Å2
MethodPISA
2
A: Cell division protein kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,4233
Polymers64,9912
Non-polymers4321
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3550 Å2
ΔGint-15 kcal/mol
Surface area23250 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.318, 135.159, 168.952
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division protein kinase 2 / p33 protein kinase


Mass: 34143.547 Da / Num. of mol.: 2 / Fragment: CDK2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A


Mass: 30847.500 Da / Num. of mol.: 2 / Fragment: UNP residues 169-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CCNA2, CCNA / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P30274
#3: Chemical ChemComp-RC8 / (2R)-2-({9-(1-methylethyl)-6-[(4-pyridin-2-ylbenzyl)amino]-9H-purin-2-yl}amino)butan-1-ol


Mass: 431.533 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H29N7O
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 134 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.26 Å3/Da / Density % sol: 62.32 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulphate, potassium chloride, Hepes, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Feb 19, 2006
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 44226 / % possible obs: 93.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 11.4
Reflection shellResolution: 2.7→2.85 Å / Rmerge(I) obs: 0.422 / Mean I/σ(I) obs: 2.8 / % possible all: 94.2

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→20 Å / Cor.coef. Fo:Fc: 0.938 / Cor.coef. Fo:Fc free: 0.893 / SU B: 29.106 / SU ML: 0.3 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.833 / ESU R Free: 0.358 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.2696 2225 5 %RANDOM
Rwork0.20997 ---
all0.21 41875 --
obs0.21298 41875 93.02 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 56.663 Å2
Baniso -1Baniso -2Baniso -3
1--1.14 Å20 Å20 Å2
2---1 Å20 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9101 0 64 134 9299
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0229403
X-RAY DIFFRACTIONr_angle_refined_deg1.2281.98212782
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.92351127
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.21823.951410
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.798151633
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.4421546
X-RAY DIFFRACTIONr_chiral_restr0.0970.21442
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.027016
X-RAY DIFFRACTIONr_nbd_refined0.2160.24718
X-RAY DIFFRACTIONr_nbtor_refined0.310.26485
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1440.2382
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1210.219
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1140.25
X-RAY DIFFRACTIONr_mcbond_it0.5331.55776
X-RAY DIFFRACTIONr_mcangle_it0.86429200
X-RAY DIFFRACTIONr_scbond_it0.96934091
X-RAY DIFFRACTIONr_scangle_it1.5924.53580
LS refinement shellResolution: 2.7→2.769 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.397 152 -
Rwork0.336 2926 -
obs--89.97 %

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