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- PDB-2r3f: Crystal Structure of Cyclin-Dependent Kinase 2 with inhibitor -

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Basic information

Entry
Database: PDB / ID: 2r3f
TitleCrystal Structure of Cyclin-Dependent Kinase 2 with inhibitor
ComponentsCell division protein kinase 2
KeywordsTRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / CELL CYCLE / INHIBITION / CYCLIN-DEPENDENT KINASE / CANCER / ATP-binding / Cell division / Mitosis / Nucleotide-binding / Phosphorylation / Polymorphism
Function / homology
Function and homology information


cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / Y chromosome / Phosphorylation of proteins involved in G1/S transition by active Cyclin E:Cdk2 complexes / positive regulation of heterochromatin formation ...cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cyclin A2-CDK2 complex / positive regulation of DNA-templated DNA replication initiation / G2 Phase / cyclin-dependent protein kinase activity / 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) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / telomere maintenance in response to DNA damage / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / cellular response to nitric oxide / 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 / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / cyclin-dependent protein kinase holoenzyme complex / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / regulation of mitotic cell cycle / post-translational protein modification / cyclin binding / positive regulation of DNA replication / male germ cell nucleus / 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 / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / Cyclin D associated events in G1 / cellular senescence / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / endosome / chromatin remodeling / protein phosphorylation / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / centrosome / DNA-templated transcription / positive regulation of cell population proliferation / 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
: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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 ...: / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; 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-SC8 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.5 Å
AuthorsFischmann, T.O. / Hruza, A.W. / Madison, V.M. / Duca, J.S.
CitationJournal: Biopolymers / Year: 2008
Title: Structure-guided discovery of cyclin-dependent kinase inhibitors.
Authors: Fischmann, T.O. / Hruza, A. / Duca, J.S. / Ramanathan, L. / Mayhood, T. / Windsor, W.T. / Le, H.V. / Guzi, T.J. / Dwyer, M.P. / Paruch, K. / Doll, R.J. / Lees, E. / Parry, D. / Seghezzi, W. / Madison, V.
History
DepositionAug 29, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 22, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Oct 30, 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_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_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: Cell division protein kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,3732
Polymers34,0031
Non-polymers3701
Water4,035224
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)53.160, 71.450, 72.160
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: 34002.527 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Production host: unidentified baculovirus / Strain (production host): SF9 / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-SC8 / 5-(2,3-dichlorophenyl)-N-(pyridin-4-ylmethyl)pyrazolo[1,5-a]pyrimidin-7-amine


Mass: 370.235 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H13Cl2N5
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 2.02 Å3/Da / Density % sol: 39.01 %
Crystal growTemperature: 298 K / Method: vapor diffusion / pH: 7.4
Details: 50 mM Na-HEPES pH 7.4, 50 mM Ammonium Acetate, 8% PEG 4000, 4% Glycerol, 1 mM TCEP, vapor diffusion, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E+ DW / Wavelength: 1.5418 Å
DetectorType: RIGAKU RAXIS IV / Detector: IMAGE PLATE / Date: Jun 1, 2002 / Details: VARIMAX MULTI-LAYER OPTICS
RadiationMonochromator: VARIMAX MULTI-LAYER OPTICS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 39402 / % possible obs: 88.2 % / Rmerge(I) obs: 0.06 / Χ2: 0.67 / Net I/σ(I): 23.3
Reflection shell
Resolution (Å)Rmerge(I) obsNum. unique allΧ2% possible all
1.5-1.510.1835480.5249.3
1.51-1.530.2116580.71760.4
1.53-1.540.2117150.69365.4
1.54-1.550.1798410.64276.1
1.55-1.570.1719010.65881.2
1.57-1.580.1749600.76587.7
1.58-1.60.17610150.73691.9
1.6-1.620.16710400.79493.3
1.62-1.630.16710520.77497.2
1.63-1.650.16310780.74598.5
1.65-1.670.15410900.73299.4
1.67-1.690.14610880.67797.6
1.69-1.710.13911090.65798.5
1.71-1.730.13810630.66397.7
1.73-1.750.12410710.64198.5
1.75-1.780.1210930.698.5
1.78-1.80.11310700.57298.1
1.8-1.830.10911070.56797.5
1.83-1.860.10210600.56497.2
1.86-1.890.110640.50596.1
1.89-1.920.09710580.51695.6
1.92-1.960.0910430.50494
1.96-20.08910500.50394.6
2-2.040.07710610.4494.5
2.04-2.080.08310100.52491.2
2.08-2.130.07210290.49392
2.13-2.180.0710070.54592
2.18-2.240.06410410.51291.7
2.24-2.310.06410170.53590.8
2.31-2.380.05810200.65992.4
2.38-2.470.05410340.72992
2.47-2.560.05410430.86792.9
2.56-2.680.05210140.88490.2
2.68-2.820.0510250.88990.5
2.82-30.05110090.95888.7
3-3.230.059740.86986
3.23-3.560.0489420.7981.3
3.56-4.070.057910.84968.7
4.07-5.130.057590.89664.7
5.13-500.0468520.92467.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PDB_EXTRACT2data extraction
BUSTER-TNTrefinement
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.5→28 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / Stereochemistry target values: Engh & Huber / Details: BUSTER-TNT
RfactorNum. reflection% reflectionSelection details
Rfree0.236 2026 -RANDOM
Rwork0.204 ---
all0.205 44781 --
obs0.205 39356 87.8 %-
Displacement parametersBiso mean: 28.444 Å2
Refinement stepCycle: LAST / Resolution: 1.5→28 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2382 0 36 224 2642

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