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- PDB-1b39: HUMAN CYCLIN-DEPENDENT KINASE 2 PHOSPHORYLATED ON THR 160 -

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Entry
Database: PDB / ID: 1b39
TitleHUMAN CYCLIN-DEPENDENT KINASE 2 PHOSPHORYLATED ON THR 160
ComponentsPROTEIN (CELL DIVISION PROTEIN KINASE 2)
KeywordsTRANSFERASE / PROTEIN KINASE / SERINE/THREONINE PROTEIN KINASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / MITOSIS / PHOSPHORYLATION
Function / homologySerine/threonine-protein kinase, active site / Orc1 removal from chromatin / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / 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) / Protein kinase-like domain superfamily ...Serine/threonine-protein kinase, active site / Orc1 removal from chromatin / Serine/Threonine protein kinases active-site signature. / Protein kinase domain profile. / 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) / Protein kinase-like domain superfamily / DNA Damage/Telomere Stress Induced Senescence / Processing of DNA double-strand break ends / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / Protein kinase domain / Regulation of TP53 Degradation / G2 Phase / Regulation of TP53 Activity through Phosphorylation / Activation of the pre-replicative complex / Protein kinase, ATP binding site / Factors involved in megakaryocyte development and platelet production / Meiotic recombination / PTK6 Regulates Cell Cycle / Protein kinase domain / 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 / Protein kinases ATP-binding region signature. / 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 protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Cajal body / condensed chromosome / cellular response to nitric oxide / cyclin binding / mitotic G1 DNA damage checkpoint / regulation of gene silencing / potassium ion transport / meiotic cell cycle / chromosome, telomeric region / G1/S 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 / regulation of G2/M transition of mitotic cell cycle / 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 / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm / Cyclin-dependent kinase 2
Function and homology information
Specimen sourceHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / 2.1 Å resolution
AuthorsBrown, N.R. / Noble, M.E.M. / Lawrie, A.M. / Morris, M.C. / Tunnah, P. / Divita, G. / Johnson, L.N. / Endicott, J.A.
Citation
Journal: J.Biol.Chem. / Year: 1999
Title: Effects of phosphorylation of threonine 160 on cyclin-dependent kinase 2 structure and activity.
Authors: Brown, N.R. / Noble, M.E. / Lawrie, A.M. / Morris, M.C. / Tunnah, P. / Divita, G. / Johnson, L.N. / Endicott, J.A.
#1: Journal: Proteins / Year: 1995
Title: Multiple Modes of Ligand Recognition: Crystal Structures of Cyclin-Dependent Protein Kinase 2 in Complex with ATP and Two Inhibitors, Olomoucine and Isopentenyladenine
Authors: Schulze-Gahmen, U. / Brandsen, J. / Jones, H.D. / Morgan, D.O. / Meijer, L. / Vesely, J. / Kim, S.H.
Validation Report
SummaryFull reportAbout validation report
DateDeposition: Dec 17, 1998 / Release: Dec 23, 1998
RevisionDateData content typeGroupProviderType
1.0Dec 23, 1998Structure modelrepositoryInitial release
1.1Apr 27, 2008Structure modelVersion format compliance
1.2Jul 13, 2011Structure modelVersion format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (CELL DIVISION PROTEIN KINASE 2)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5343
Polyers34,0031
Non-polymers5312
Water2,612145
1


TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
γ
α
β
Length a, b, c (Å)53.420, 71.660, 72.520
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP 21 21 21

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Components

#1: Protein/peptide PROTEIN (CELL DIVISION PROTEIN KINASE 2) / EC 2.7.1 , TRANSFERASE / P33 PROTEIN KINASE


Mass: 34002.527 Da / Num. of mol.: 1 / Fragment: INTACT / Source: (gene. exp.) Homo sapiens (human) / Genus: Homo / Plasmid name: BACULOVIRUSBaculoviridae / Genus (production host): Spodoptera / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Formula: Mg / Magnesium
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Formula: C10H16N5O13P3 / Adenosine triphosphate / Comment: ATP (energy-carrying molecule) *YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 145 / 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: 2.04 / Density percent sol: 45 %
Crystal growMethod: streak seeding / pH: 7.5
Details: STREAK SEEDING FROM UNPHOSPHORYLATED CDK2 CRYSTALS, USING PHOSPHORYLATED CDK2 PROTEIN PREEQUILIBRATED AGAINST WELL SOLUTION. PROTEIN AT 10 MG/ML IN 50MM TRIS/HCL PH7.5, 50MM NACL. WELL SOLUTION OF 12-16% PEG 3350, 0.1M TRIS/HCL PH 7.5, 50MM AMMONIUM ACETATE., streak seeding
Crystal grow
*PLUS
Method: vapor diffusion, sitting drop
components of the solutions
*PLUS
IDConcCommon nameCrystal IDSol ID
112-16 %PEG40001reservoir
20.1 MTris-HCl1reservoir
350 mMammonium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 kelvins
SourceSource: SYNCHROTRON / Type: EMBL/DESY, HAMBURG BEAMLINE BW7B / Synchrotron site: EMBL/DESY, Hamburg / Beamline: BW7B / Wavelength: 1.044
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE
RadiationDiffraction protocol: SINGLE WAVELENGTH / Monochromatic or laue m l: M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.044 Å / Relative weight: 1
ReflectionD resolution high: 2.1 Å / D resolution low: 20 Å / Number obs: 15947 / Observed criterion sigma I: 0 / Rmerge I obs: 0.12 / NetI over sigmaI: 4.1 / Redundancy: 4.4 % / Percent possible obs: 96.3
Reflection shellRmerge I obs: 0.38 / Highest resolution: 2.1 Å / Lowest resolution: 2.23 Å / MeanI over sigI obs: 2 / Percent possible all: 97.2
Reflection
*PLUS
Number measured all: 70130
Reflection shell
*PLUS
Percent possible obs: 97.2

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Processing

Software
NameVersionClassification
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefineMethod to determine structure: OTHER
Starting model: UNPUBLISHED

R Free selection details: RANDOM 5% / Cross valid method: FREE-R / Sigma F: 0
Least-squares processR factor R free: 0.27 / R factor R work: 0.2 / Highest resolution: 2.1 Å / Lowest resolution: 2 Å / Number reflection obs: 15947 / Percent reflection R free: 5 / Percent reflection obs: 96
Refine hist #LASTHighest resolution: 2.1 Å / Lowest resolution: 2 Å
Number of atoms included #LASTProtein: 2338 / Nucleic acid: 0 / Ligand: 32 / Solvent: 145 / Total: 2515
Refine LS restraints
Refine IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.020.02
X-RAY DIFFRACTIONp_angle_d0.0490.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0440.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr.172.15
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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