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- PDB-1oiy: Structure of human Thr160-phospho CDK2/cyclin A complexed with a ... -

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Basic information

Entry
Database: PDB / ID: 1oiy
TitleStructure of human Thr160-phospho CDK2/cyclin A complexed with a 6-cyclohexylmethyloxy-2-anilino-purine inhibitor
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A2
KeywordsKINASE / TRANSFERASE / SERINE/THREONINE-PROTEIN KINASE / ATP-BINDING / CELL CYCLE / CELL DIVISION / MITOSIS / PHOSPHORYLATION
Function / homology
Function and homology information


cellular response to luteinizing hormone stimulus / cellular response to cocaine / cell cycle G1/S phase transition / mitotic cell cycle phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin 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 / mitotic cell cycle phase transition / male pronucleus / female pronucleus / cellular response to insulin-like growth factor stimulus / cellular response to leptin 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 / condensed chromosome / cyclin-dependent protein kinase holoenzyme complex / Cajal body / 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 / G2/M transition of mitotic cell cycle / transcription factor complex / regulation of signal transduction by p53 class mediator / DNA replication / endosome / peptidyl-serine phosphorylation / protein deubiquitination / centrosome / cell division / DNA repair / protein domain specific binding / protein serine/threonine kinase activity / protein phosphorylation / viral process / positive regulation of cell population proliferation / protein kinase binding / positive regulation of transcription, DNA-templated / negative regulation of transcription by RNA polymerase II / magnesium ion binding / 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: 2.4 Å
AuthorsPratt, D.J. / Endicott, J.A. / Noble, M.E.M.
CitationJournal: J.Med.Chem. / Year: 2004
Title: N2-Substituted O6-Cyclohexylmethylguanine Derivatives: Potent Inhibitors of Cyclin-Dependent Kinases 1 and 2
Authors: Hardcastle, I.R. / Arris, C.E. / Bentley, J. / Boyle, F.T. / Chen, Y. / Curtin, N.J. / Endicott, J.A. / Gibson, A.E. / Golding, B.T. / Griffin, R.J. / Jewsbury, P. / Menyerol, J. / Mesguiche, V. / Newell, D.R. / Noble, M.E.M. / Pratt, D.J. / Wang, L.-Z. / Whitfield, H.J.
Validation Report
SummaryFull reportAbout validation report
History
DepositionJun 26, 2003Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 13, 2004Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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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)129,4529
Polymers128,4794
Non-polymers9735
Water5,008278
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7385
Polymers64,2392
Non-polymers4993
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)64,7144
Polymers64,2392
Non-polymers4752
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
γ
α
β
Length a, b, c (Å)73.997, 134.872, 147.865
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper:

Code: given

IDMatrixVector
1(-0.00589, -0.49617, 0.8682), (-0.53155, -0.73385, -0.423), (0.84701, -0.46398, -0.25942)11.16755, 142.41133, 71.70934
2(-0.00142, -0.49692, 0.86779), (-0.53482, -0.73288, -0.42054), (0.84497, -0.46471, -0.26472)11.30206, 142.49719, 71.42867

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Components

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Protein/peptide , 2 types, 4 molecules ACBD

#1: Protein/peptide CELL DIVISION PROTEIN KINASE 2 / / P33 PROTEIN KINASE / CDK2


Mass: 34354.770 Da / Num. of mol.: 2 / Details: PHOSPHORYLATED ON THR160
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24941, EC: 2.7.1.37
#2: Protein/peptide CYCLIN A2 / / CYCLIN A / CCNA2 / CCNA / CCN1


Mass: 29884.605 Da / Num. of mol.: 2 / Fragment: RESIDUES 174-432
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248

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Non-polymers , 4 types, 283 molecules

#3: Chemical ChemComp-N41 / 4-(6-CYCLOHEXYLMETHOXY-9H-PURIN-2-YLAMINO)--BENZAMIDE


Mass: 366.417 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C19H22N6O2
#4: Chemical ChemComp-SGM / MONOTHIOGLYCEROL


Mass: 108.159 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O2S / 3-Mercaptopropane-1,2-diol
#5: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Magnesium
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 278 / Source method: isolated from a natural source / Formula: H2O / Water

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Details

Compound detailsCYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITIONS. KINASE ...CYCLIN CONTROLS THE CELL CYCLE AT THE G1/S (START) AND THE G2/M (MITOSIS) TRANSITIONS. KINASE INTERACTS WITH CYCLINS A, D, OR E. ACTIVITY OF CDK2 IS MAXIMAL DURING S PHASE AND G2.

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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: 2.8 Å3/Da / Density % sol: 55.6 % / Description: USED DATA TO 3.5 A FOR MR
Crystal growpH: 7
Details: 0.7-0.85 M POTASSIUM CHLORIDE, 1.1-1.25 M AMMONIUM SULFATE, 40 MM HEPES, PH 7.0, 5 MM DITHIOTHREITOL, 10 MG/ML PROTEIN, 8M SODIUM FORMATE CRYO-PROTECTANT

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9393
DetectorType: ADSC CCD / Detector: CCD / Date: May 10, 2003
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9393 Å / Relative weight: 1
ReflectionResolution: 2.4→47.14 Å / Num. obs: 53738 / % possible obs: 92.3 % / Observed criterion σ(I): 1 / Redundancy: 2.27 % / Rmerge(I) obs: 0.105 / Net I/σ(I): 5.0142
Reflection shellResolution: 2.4→2.53 Å / Redundancy: 1.83 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 2.56 / % possible all: 80.3

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1H1S
Resolution: 2.4→100 Å / Cor.coef. Fo:Fc: 0.893 / Cor.coef. Fo:Fc free: 0.822 / SU B: 10.77 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.501 / ESU R Free: 0.332 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.309 2717 5.1 %RANDOM
Rwork0.244 ---
Obs-50989 91.6 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 37.11 Å2
Baniso -1Baniso -2Baniso -3
1--2.52 Å20 Å20 Å2
2--0.4 Å20 Å2
3---2.12 Å2
Refinement stepCycle: LAST / Resolution: 2.4→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8918 0 67 278 9263
Refine LS restraints

Refinement-ID: X-RAY DIFFRACTION

TypeDev idealDev ideal targetNumber
r_bond_refined_d0.0160.0229221
r_bond_other_d
r_angle_refined_deg1.7241.97912520
r_angle_other_deg
r_dihedral_angle_1_deg6.78751102
r_dihedral_angle_2_deg
r_dihedral_angle_3_deg
r_dihedral_angle_4_deg
r_chiral_restr0.1130.21414
r_gen_planes_refined0.0060.026830
r_gen_planes_other
r_nbd_refined0.2510.25243
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined0.2190.2596
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined0.2620.245
r_symmetry_vdw_other
r_symmetry_hbond_refined0.2620.27
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_mcbond_it0.7861.55549
r_mcbond_other
r_mcangle_it1.46229028
r_mcangle_other
r_scbond_it2.2533672
r_scbond_other
r_scangle_it3.6484.53492
r_scangle_other
r_long_range_B_refined
r_long_range_B_other
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded
LS refinement shellResolution: 2.4→2.46 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.401 174
Rwork0.322 3138

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