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- PDB-1fvv: THE STRUCTURE OF CDK2/CYCLIN A IN COMPLEX WITH AN OXINDOLE INHIBITOR -

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Basic information

Entry
Database: PDB / ID: 1fvv
TitleTHE STRUCTURE OF CDK2/CYCLIN A IN COMPLEX WITH AN OXINDOLE INHIBITOR
Components
  • CYCLIN A
  • CYCLIN-DEPENDENT KINASE 2
KeywordsTRANSFERASE / CELL CYCLE / cyclin-dependent kinase / cyclin A
Function / homology
Function and homology information


: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon ...: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / positive regulation of DNA biosynthetic process / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / 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 / Y chromosome / cyclin-dependent protein kinase activity / 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 / microtubule organizing center / regulation of DNA replication / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / 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 / Cajal body / 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 / 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 / cellular response to platelet-derived growth factor stimulus / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / cellular response to estradiol stimulus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / DNA Damage/Telomere Stress Induced Senescence / potassium ion transport / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / 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 / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / cellular response to hypoxia / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / chromosome, telomeric region / DNA replication / protein phosphorylation / endosome / Ub-specific processing proteases / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA-templated transcription / centrosome / protein kinase binding
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-like / Cyclin, C-terminal domain / Cyclin_C ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / 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-107 / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.8 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 / Item: _software.classification / _software.name
Revision 1.4Feb 7, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: CYCLIN-DEPENDENT KINASE 2
B: CYCLIN A
C: CYCLIN-DEPENDENT KINASE 2
D: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,5876
Polymers127,6884
Non-polymers8992
Water2,324129
1
A: CYCLIN-DEPENDENT KINASE 2
B: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2943
Polymers63,8442
Non-polymers4501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4240 Å2
ΔGint-16 kcal/mol
Surface area23680 Å2
MethodPISA
2
C: CYCLIN-DEPENDENT KINASE 2
D: CYCLIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,2943
Polymers63,8442
Non-polymers4501
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-17 kcal/mol
Surface area22910 Å2
MethodPISA
Unit cell
Length a, b, c (Å)184.952, 184.952, 212.832
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Cell settinghexagonal
Space group name H-MP6222

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Components

#1: Protein CYCLIN-DEPENDENT KINASE 2 / E.C.2.7.1.37 / CDK2 / P33 PROTEIN KINASE


Mass: 33976.488 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Plasmid: PFASTBAC1 OR PACHLT-A / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, EC: 2.7.1.37
#2: Protein CYCLIN A / CYCLIN A2


Mass: 29867.512 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P20248
#3: Chemical ChemComp-107 / 4-[(7-OXO-7H-THIAZOLO[5,4-E]INDOL-8-YLMETHYL)-AMINO]-N-PYRIDIN-2-YL-BENZENESULFONAMIDE


Mass: 449.506 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H15N5O3S2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 129 / 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: 4.11 Å3/Da / Density % sol: 70.09 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.7
Details: 1.5 M sodium acetate, 100 mM sodium cacodylate, pH 6.7, VAPOR DIFFUSION, HANGING DROP, temperature 277K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7.5 / 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: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1
DetectorType: MARRESEARCH / Detector: CCD / Date: Jan 3, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→20 Å / Num. all: 50936 / Num. obs: 50936 / % possible obs: 95.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 10 % / Biso Wilson estimate: 91.3 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 36
Reflection shellResolution: 2.8→2.98 Å / Redundancy: 9 % / Rmerge(I) obs: 0.29 / Num. unique all: 7029 / % possible all: 90.2
Reflection
*PLUS
Num. measured all: 541713 / Rmerge(I) obs: 0.07

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Processing

Software
NameClassification
CNSrefinement
MAR345data collection
HKL-2000data scaling
CNSphasing
RefinementResolution: 2.8→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.26 5137 10 %random
Rwork0.26 ---
all0.21 50936 --
obs0.21 50936 95.9 %-
Refinement stepCycle: LAST / Resolution: 2.8→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8960 0 62 129 9151
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg0.01
X-RAY DIFFRACTIONc_bond_d1.7
Software
*PLUS
Name: CNS / Classification: refinement
Refinement
*PLUS
Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor Rfree: 0.26 / Rfactor Rwork: 0.26
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.009
X-RAY DIFFRACTIONc_angle_deg1.39

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