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- PDB-2bkz: STRUCTURE OF CDK2-CYCLIN A WITH PHA-404611 -

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Basic information

Entry
Database: PDB / ID: 2bkz
TitleSTRUCTURE OF CDK2-CYCLIN A WITH PHA-404611
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
KeywordsTRANSFERASE / TRANSFERASE-COMPLEX / PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE / PHOSPHORYLATION / CELL DIVISION / CYCLIN / ATP-BINDING / CELL CYCLE / MITOSIS / POLYMORPHISM
Function / homology
Function and homology information


Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / 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 / response to glucagon ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / 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 / response to glucagon / cellular response to cocaine / cyclin-dependent protein serine/threonine kinase regulator activity / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / 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 / regulation of DNA replication / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / animal organ regeneration / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Activation of ATR in response to replication stress / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / meiotic cell cycle / male germ cell nucleus / response to organic substance / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / positive regulation of fibroblast proliferation / 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 / cellular response to hypoxia / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / Ub-specific processing proteases / endosome / chromatin remodeling / cell division / protein domain specific binding / protein phosphorylation / DNA repair / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / protein kinase binding / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II
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, C-terminal domain / Cyclin_C / Cyclin-like ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin, C-terminal domain / Cyclin_C / Cyclin-like / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / 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-SBC / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.6 Å
AuthorsDAlessio, R. / Bargiottia, A. / Metz, S. / Brasca, M.G. / Cameron, A. / Ermoli, A. / Marsiglio, A. / Polucci, P. / Roletto, F. / Tibolla, M. ...DAlessio, R. / Bargiottia, A. / Metz, S. / Brasca, M.G. / Cameron, A. / Ermoli, A. / Marsiglio, A. / Polucci, P. / Roletto, F. / Tibolla, M. / Vazquez, M.L. / Vulpetti, A. / Pevarello, P.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2005
Title: Benzodipyrazoles: A New Class of Potent Cdk2 Inhibitors
Authors: Dalessio, R. / Bargiottia, A. / Metz, S. / Brasca, M.G. / Cameron, A. / Ermoli, A. / Marsiglio, A. / Polucci, P. / Roletto, F. / Tibolla, M. / Vazquez, M.L. / Vulpetti, A. / Pevarello, P.
History
DepositionFeb 23, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 8, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Apr 3, 2019Group: Data collection / Other / Source and taxonomy
Category: entity_src_gen / pdbx_database_proc / pdbx_database_status
Item: _entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_cell_line / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _pdbx_database_status.recvd_author_approval

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)131,9678
Polymers131,0624
Non-polymers9054
Water4,900272
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9834
Polymers65,5312
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,9834
Polymers65,5312
Non-polymers4522
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)183.862, 183.862, 214.572
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(-0.21824, -0.87436, 0.43343), (-0.87804, -0.01792, -0.47826), (0.42594, -0.48494, -0.76381)93.50958, 219.20874, 276.95099
2given(-0.24625, -0.86671, 0.4338), (-0.85948, -0.01158, -0.51104), (0.44794, -0.49869, -0.74206)91.17916, 221.1532, 278.16428

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / / P33 PROTEIN KINASE


Mass: 35251.883 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Cell line (production host): High Five / Production host: TRICHOPLUSIA NI (cabbage looper) / References: UniProt: P24941, EC: 2.7.1.37
#2: Protein CYCLIN A2 / / CYCLIN A


Mass: 30278.967 Da / Num. of mol.: 2 / Fragment: RESIDUES 174-432 (C-TERMINAL PORTION)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX6P / Production host: ESCHERICHIA COLI BL21 (bacteria) / References: UniProt: P20248
#3: Chemical ChemComp-SBC / 1-[4-(AMINOSULFONYL)PHENYL]-1,6-DIHYDROPYRAZOLO[3,4-E]INDAZOLE-3-CARBOXAMIDE / 1-(4-SULFAMOYL-PHENYL)-1,4,5,6-TETRAHYDRO-BENZO-DIPYRAZOLE-3-CARBOXYLIC ACID AMIDE


Mass: 356.359 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C15H12N6O3S
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 272 / Source method: isolated from a natural source / Formula: H2O
Compound detailsFUNCTION: CELL DIVISION PROTEIN KINASE 2 HAS A POSSIBLE INVOLVEMENT IN THE CONTROL OF THE CELL ...FUNCTION: CELL DIVISION PROTEIN KINASE 2 HAS A POSSIBLE INVOLVEMENT IN THE CONTROL OF THE CELL CYCLE. CYCLIN A2 IS ESSENTIAL FOR THE CONTROL OF THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITIONS
Sequence details5 AMINO ACIDS EXTRA AT THE N-TERMINUS DUE TO CLONING PROTOCOL

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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: 4.02 Å3/Da / Density % sol: 69.18 %
Crystal growpH: 7 / Details: 20% AMMONIUM SULPHATE, 1M KCL, 40MM HEPES PH 7

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Feb 22, 2001
RadiationMonochromator: DIAMOND (111), GE(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→30 Å / Num. obs: 66033 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 4 % / Biso Wilson estimate: 38.5 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 18.2
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 3 / % possible all: 99.8

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Processing

Software
NameVersionClassification
CNX2002refinement
DENZOdata reduction
SCALEPACKdata scaling
RefinementMethod to determine structure: OTHER / Resolution: 2.6→29.8 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: BFACTOR_MODEL / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. THERE IS A FEATURE IN THE ELECTRON DENSITY MAP ATTACHED TO ASP 28 OF BOTH CDK2 MOLECULES THAT COULD NOT ANY MOLECULE IN THE CRYSTALLISATION MIXTURE. THIS HAS BEEN ...Details: BULK SOLVENT MODEL USED. THERE IS A FEATURE IN THE ELECTRON DENSITY MAP ATTACHED TO ASP 28 OF BOTH CDK2 MOLECULES THAT COULD NOT ANY MOLECULE IN THE CRYSTALLISATION MIXTURE. THIS HAS BEEN MODELLED BY WATER MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.259 1319 2 %RANDOM
Rwork0.23 ---
obs-65870 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.301 Å2 / ksol: 0.344039 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1-5.87 Å29.25 Å20 Å2
2--5.87 Å20 Å2
3----11.74 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.42 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.39 Å
Refinement stepCycle: LAST / Resolution: 2.6→29.8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8963 0 60 272 9295
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d20.8
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.83
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
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.023 / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.342 2 %
Rwork0.307 -
obs-99.9 %
Xplor fileSerial no: 1 / Param file: PROTEIN_REP.PARAM / Topol file: 404.TOP

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