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

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Basic information

Entry
Database: PDB / ID: 1fvt
TitleTHE STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 (CDK2) IN COMPLEX WITH AN OXINDOLE INHIBITOR
ComponentsCELL DIVISION PROTEIN KINASE 2
KeywordsTRANSFERASE / CELL CYCLE / cyclin-dependent kinase / oxindole
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 / G0 and Early G1 / Telomere Extension By Telomerase / 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 / mitotic G1 DNA damage checkpoint signaling / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / 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 / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / G1/S transition of mitotic cell cycle / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / 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) / peptidyl-serine phosphorylation / regulation of gene expression / 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-106 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / Resolution: 2.2 Å
AuthorsDavis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. ...Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr., R.T. / Griffin, R.J. / Harris, P.A. / Hassell, A.M. / Holmes, W.D. / Hunter, R.N. / Knick, V.B. / Lackey, K. / Lovejoy, B. / Luzzio, M.J. / Murray, D. / Parker, P. / Rocque, W.J. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.K.
CitationJournal: Science / Year: 2001
Title: Prevention of chemotherapy-induced alopecia in rats by CDK inhibitors.
Authors: Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr, R.T. / Griffin, R.J. / Harris, P.A. / ...Authors: Davis, S.T. / Benson, B.G. / Bramson, H.N. / Chapman, D.E. / Dickerson, S.H. / Dold, K.M. / Eberwein, D.J. / Edelstein, M. / Frye, S.V. / Gampe Jr, R.T. / Griffin, R.J. / Harris, P.A. / Hassell, A.M. / Holmes, W.D. / Hunter, R.N. / Knick, V.B. / Lackey, K. / Lovejoy, B. / Luzzio, M.J. / Murray, D. / Parker, P. / Rocque, W.J. / Shewchuk, L. / Veal, J.M. / Walker, D.H. / Kuyper, L.F.
History
DepositionSep 20, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 17, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 4, 2017Group: Refinement description / Category: software
Revision 2.0Sep 16, 2020Group: Derived calculations / Non-polymer description / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_entity_nonpoly / struct_site
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.name / _entity.formula_weight / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 2.1Feb 7, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)34,3722
Polymers33,9761
Non-polymers3951
Water1,45981
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)54.142, 72.711, 72.933
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Cell settingorthorhombic
Space group name H-MP212121

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / E.C.2.7.1.37 / CDK2 / P33 PROTEIN KINASE


Mass: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid details: BACILOVIRUS / Plasmid: PFASTBAC1 OR PACHLT-A / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, EC: 2.7.1.37
#2: Chemical ChemComp-106 / 4-[(2Z)-2-(5-bromo-2-oxo-1,2-dihydro-3H-indol-3-ylidene)hydrazinyl]benzene-1-sulfonamide


Mass: 395.231 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C14H11BrN4O3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 81 / Source method: isolated from a natural source / Formula: H2O

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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: 2.11 Å3/Da / Density % sol: 41.74 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3340, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K
Crystal grow
*PLUS
Temperature: 20 ℃ / Details: Shewchuk L., (2000) J. Med. Chem., 43, 133.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
220 mMHEPES1drop
31 mMEDTA1drop
410 %PEG33401reservoir

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Data collection

DiffractionMean temperature: 300 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418
DetectorType: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Apr 11, 1997
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.2→28 Å / Num. all: 13325 / Num. obs: 13325 / % possible obs: 87.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 11 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.071 / Net I/σ(I): 41.2
Reflection shellResolution: 2.2→2.34 Å / Redundancy: 7.8 % / Rmerge(I) obs: 0.217 / Num. unique all: 2013 / % possible all: 87
Reflection
*PLUS
Num. measured all: 157652

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Processing

Software
NameClassification
X-PLORmodel building
CNSrefinement
SCALEPACKdata scaling
X-PLORphasing
RefinementResolution: 2.2→30 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.232 1219 9.1 %random
Rwork0.232 ---
all0.195 13325 --
obs0.195 13325 87.9 %-
Refinement stepCycle: LAST / Resolution: 2.2→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2262 0 23 81 2366
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_bond_d0.009
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 9.1 %
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Type: c_angle_deg / Dev ideal: 1.4

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