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- PDB-2c4g: STRUCTURE OF CDK2-CYCLIN A WITH PHA-533514 -

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Basic information

Entry
Database: PDB / ID: 2c4g
TitleSTRUCTURE OF CDK2-CYCLIN A WITH PHA-533514
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
KeywordsTRANSFERASE / PROTEIN KINASE / SERINE/THREONINE-PROTEIN KINASE / PHOSPHORYLATION / CELL DIVISION / CYCLIN / ATP-BINDING / CELL CYCLE / MITOSIS / NUCLEOTIDE-BINDING / POLYMORPHISM
Function / homology
Function and homology information


cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / male pronucleus / mitotic cell cycle phase transition / female pronucleus / cellular response to leptin stimulus / cellular response to insulin-like growth factor stimulus / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity ...cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / male pronucleus / mitotic cell cycle phase transition / female pronucleus / cellular response to leptin stimulus / cellular response to insulin-like growth factor stimulus / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / cochlea development / cellular response to platelet-derived growth factor stimulus / regulation of DNA replication / regulation of cyclin-dependent protein serine/threonine kinase activity / cyclin A1-CDK2 complex / cyclin E1-CDK2 complex / cyclin E2-CDK2 complex / positive regulation of DNA-dependent DNA replication initiation / cyclin A2-CDK2 complex / Y chromosome / cyclin-dependent protein kinase activity / X chromosome / histone phosphorylation / centrosome duplication / centriole replication / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / Cajal body / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / cellular response to nitric oxide / mitotic G1 DNA damage checkpoint / cyclin binding / regulation of gene silencing / potassium ion transport / meiotic cell cycle / cellular response to estradiol stimulus / chromosome, telomeric region / animal organ regeneration / G1/S transition of mitotic cell cycle / positive regulation of fibroblast proliferation / anaphase-promoting complex-dependent catabolic process / regulation of G2/M transition of mitotic cell cycle / DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest / cellular response to hypoxia / Ras protein signal transduction / transcription factor complex / G2/M transition of mitotic cell cycle / regulation of signal transduction by p53 class mediator / DNA replication / regulation of gene expression / endosome / protein deubiquitination / peptidyl-serine phosphorylation / cell division / centrosome / DNA repair / multicellular organism development / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / positive regulation of cell population proliferation / viral process / protein kinase binding / positive regulation of transcription, DNA-templated / magnesium ion binding / negative regulation of transcription by RNA polymerase II / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm
Protein kinase-like domain superfamily / Cyclin-A, N-terminal / Protein kinase domain / Cyclin, C-terminal domain / Cyclin, N-terminal / Serine/threonine-protein kinase, active site / Protein kinase, ATP binding site / Cyclin-like / Cyclin-like superfamily / Cyclin ...Protein kinase-like domain superfamily / Cyclin-A, N-terminal / Protein kinase domain / Cyclin, C-terminal domain / Cyclin, N-terminal / Serine/threonine-protein kinase, active site / Protein kinase, ATP binding site / Cyclin-like / Cyclin-like superfamily / Cyclin / Protein kinase domain / Cyclin, N-terminal domain / Cyclin, C-terminal domain / Cyclin-like / Cyclin A; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); domain 1 / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / 2-Layer Sandwich / Orthogonal Bundle / Mainly Alpha / Alpha Beta
Cyclin-dependent kinase 2 / Cyclin-A2
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCameron, A. / Fogliatto, G. / Pevarello, P. / Fancelli, D. / Vulpetti, A. / Amici, R. / Villa, M. / Pittala, V. / Ciomei, M. / Mercurio, C. / Bischoff, J.R. / Roletto, F. / Varasi, M. / Brasca, M.G.
CitationJournal: Bioorg.Med.Chem.Lett. / Year: 2006
Title: 3-Amino-1,4,5,6-Tetrahydropyrrolo[3,4-C]Pyrazoles: A New Class of Cdk2 Inhibitors.
Authors: Pevarello, P. / Fancelli, D. / Vulpetti, A. / Amici, R. / Villa, M. / Pittala, V. / Vianello, P. / Cameron, A. / Ciomei, M. / Mercurio, C. / Bischoff, J.R. / Roletto, F. / Varasi, M. / Brasca, M.G.
Validation Report
SummaryFull reportAbout validation report
History
DepositionOct 19, 2005Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 23, 2005Provider: repository / Type: Initial release
Revision 1.1May 7, 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)131,7888
Polymers131,0624
Non-polymers7274
Water2,486138
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8944
Polymers65,5312
Non-polymers3632
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)65,8944
Polymers65,5312
Non-polymers3632
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)191.985, 191.985, 205.880
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.37982, -0.82165, 0.425), (-0.79481, 0.0548, -0.60438), (0.4733, -0.56736, -0.67387)
Vector: 86.90833, 220.52824, 276.81595)

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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 173-432 (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-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: Chemical ChemComp-514 / (3Z)-5-ACETYL-3-(BENZOYLIMINO)-3,6-DIHYDROPYRROLO[3,4-C]PYRAZOL-5-IUM


Mass: 267.263 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H11N4O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 138 / Source method: isolated from a natural source / Formula: H2O
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 Å3/Da / Density % sol: 0.64 %
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: ID14-2 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Nov 20, 2003 / Details: TOROIDAL MIRROR
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: 2.7→30 Å / Num. obs: 61565 / % possible obs: 99.7 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 61.9 Å2 / Rmerge(I) obs: 0.08 / Net I/σ(I): 17
Reflection shellResolution: 2.7→2.8 Å / Redundancy: 5.1 % / Rmerge(I) obs: 0.7 / Mean I/σ(I) obs: 2.4 / % possible all: 99.4

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Processing

Software
NameVersionClassification
CNX2002refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1FIN
Resolution: 2.7→29.93 Å / Rfactor Rfree error: 0.007 / Isotropic thermal model: BFACTOR_MODEL / Cross valid method: THROUGHOUT / σ(F): 0
Details: BULK SOLVENT MODEL USED. UNIDENTIFIED DENSITY SEEN NEAR TO RESIDUE GLU 28 HAS BEEN MODELLED WITH WATER MOLECULES.
RfactorNum. reflection% reflectionSelection details
Rfree0.25 1233 2 %RANDOM
Rwork0.233 ---
Obs-61411 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.3764 Å2 / ksol: 0.340186 e/Å3
Displacement parametersBiso mean: 70.1 Å2
Baniso -1Baniso -2Baniso -3
1-4.46 Å211.08 Å20 Å2
2--4.46 Å20 Å2
3----8.92 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.4 Å
Luzzati d res low-5 Å
Luzzati sigma a0.56 Å0.48 Å
Refinement stepCycle: LAST / Resolution: 2.7→29.93 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8999 0 50 138 9187
Refine LS restraints
Refinement-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
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_d21
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
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
Refine LS restraints NCSNCS model details: RESTRAINTS / Rms dev position: 0.2 Å / Weight position: 150
LS refinement shellResolution: 2.7→2.87 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6 /
Rfactor% reflection
Rfree0.403 2 %
Rwork0.339 -
Obs-99.2 %
Xplor fileSerial no: 1 / Param file: PROTEIN_TPO.PARAM / Topol file: 514.TOP

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