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- PDB-1di8: THE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH... -

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Basic information

Entry
Database: PDB / ID: 1di8
TitleTHE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH 4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE
ComponentsCYCLIN-DEPENDENT KINASE 2
KeywordsTRANSFERASE / SERINE/THREONINE PROTEIN KINASE / CELL CYCLE / ATP-BINDING
Function / homology
Function and homology information


Orc1 removal from chromatin / G0 and Early G1 / Activation of ATR in response to replication stress / Regulation of APC/C activators between G1/S and early anaphase / SCF(Skp2)-mediated degradation of p27/p21 / Senescence-Associated Secretory Phenotype (SASP) / DNA Damage/Telomere Stress Induced Senescence / Processing of DNA double-strand break ends / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of TP53 Degradation ...Orc1 removal from chromatin / G0 and Early G1 / Activation of ATR in response to replication stress / Regulation of APC/C activators between G1/S and early anaphase / SCF(Skp2)-mediated degradation of p27/p21 / Senescence-Associated Secretory Phenotype (SASP) / DNA Damage/Telomere Stress Induced Senescence / Processing of DNA double-strand break ends / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Regulation of TP53 Degradation / G2 Phase / Regulation of TP53 Activity through Phosphorylation / Activation of the pre-replicative complex / Factors involved in megakaryocyte development and platelet production / Meiotic recombination / PTK6 Regulates Cell Cycle / CDK-mediated phosphorylation and removal of Cdc6 / Cyclin A:Cdk2-associated events at S phase entry / p53-Dependent G1 DNA Damage Response / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin E associated events during G1/S transition / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / Cajal body / cellular response to nitric oxide / mitotic G1 DNA damage checkpoint / cyclin binding / regulation of gene silencing / potassium ion transport / meiotic cell cycle / chromosome, telomeric region / G1/S transition of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / anaphase-promoting complex-dependent catabolic process / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / Ras protein signal transduction / transcription factor complex / G2/M transition of mitotic cell cycle / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / centrosome / cell division / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / positive regulation of transcription, DNA-templated / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Serine/threonine-protein kinase, active site / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / Protein kinase-like domain superfamily / Protein kinase domain / Protein kinase, ATP binding site / Protein kinase domain / Protein kinases ATP-binding region signature.
Cyclin-dependent kinase 2
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsShewchuk, L. / Hassell, A. / Kuyper, L.F.
CitationJournal: J.Med.Chem. / Year: 2000
Title: Binding mode of the 4-anilinoquinazoline class of protein kinase inhibitor: X-ray crystallographic studies of 4-anilinoquinazolines bound to cyclin-dependent kinase 2 and p38 kinase.
Authors: Shewchuk, L. / Hassell, A. / Wisely, B. / Rocque, W. / Holmes, W. / Veal, J. / Kuyper, L.F.
Validation Report
SummaryFull reportAbout validation report
History
DepositionNov 29, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 29, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CYCLIN-DEPENDENT KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,2742
Polymers33,9761
Non-polymers2971
Water2,036113
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)72.752, 74.076, 54.005
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/peptide CYCLIN-DEPENDENT KINASE 2 / / CDK2


Mass: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Cell (production host): T.NI / Production host: unidentified baculovirus
References: UniProt: P24941, Transferases, Transferring phosphorus-containing groups, Phosphotransferases with an alcohol group as acceptor
#2: Chemical ChemComp-DTQ / 4-[3-HYDROXYANILINO]-6,7-DIMETHOXYQUINAZOLINE


Mass: 297.309 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C16H15N3O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 113 / Source method: isolated from a natural source / Formula: H2O / Water

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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: 2.14 Å3/Da / Density % sol: 42.53 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20MM HEPES, 1MM EDTA, 10% PEG3350, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS

Crystal-ID: 1

IDConc.Common nameSol-IDDetails
110 mg/mlproteindrop
220 mMHEPESdroppH7.5
31 mMEDTAdrop
410 %PEG3340reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: Feb 16, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 17097 / Num. obs: 14980 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 10 % / Biso Wilson estimate: 14 Å2 / Rmerge(I) obs: 0.088 / Net I/σ(I): 36
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 10 % / Rmerge(I) obs: 0.2 / % possible all: 96.3
Reflection
*PLUS
Num. measured all: 160386 / Rmerge(I) obs: 0.093

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement
CNSphasing
RefinementResolution: 2.2→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: ENGH & HUBER
RfactorNum. reflectionSelection details
Rfree0.226 -RANDOM
Rwork0.186 --
All-17097 -
Obs-14980 -
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 22 113 2397
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.01
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 10 Å / σ(F): 0 / Rfactor obs: 0.185 / Rfactor Rfree: 0.227
Refine LS restraints
*PLUS
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.3

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