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- PDB-3bhu: Structure of phosphorylated Thr160 CDK2/cyclin A in complex with ... -

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Basic information

Entry
Database: PDB / ID: 3bhu
TitleStructure of phosphorylated Thr160 CDK2/cyclin A in complex with the inhibitor meriolin 5
Components
  • Cell division protein kinase 2
  • Cyclin-A2
KeywordsTRANSFERASE / Ser/Thr protein kinase / phosphorylation / cell cycle / ATP-binding / Cell division / Mitosis / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Cyclin
Function / homology
Function and homology information


cell cycle G1/S phase transition / mitotic cell cycle phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / 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 ...cell cycle G1/S phase transition / mitotic cell cycle phase transition / cyclin-dependent protein serine/threonine kinase regulator activity / 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 / 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 / telomere maintenance in response to DNA damage / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / 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 / 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 / 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 / Meiotic recombination / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / G2/M transition of mitotic cell cycle / 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 / Senescence-Associated Secretory Phenotype (SASP) / regulation of gene expression / peptidyl-serine phosphorylation / 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
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-MHR / Cyclin-dependent kinase 2 / Cyclin-A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.3 Å
AuthorsEchalier, A. / Bettayeb, K. / Ferandin, Y. / Lozach, O. / Clement, M. / Valette, A. / Liger, F. / Marquet, B. / Morris, J.C. / Endicott, J.A. ...Echalier, A. / Bettayeb, K. / Ferandin, Y. / Lozach, O. / Clement, M. / Valette, A. / Liger, F. / Marquet, B. / Morris, J.C. / Endicott, J.A. / Joseph, B. / Meijer, L.
CitationJournal: Cancer Res. / Year: 2007
Title: Meriolins, a new class of cell death inducing kinase inhibitors with enhanced selectivity for cyclin-dependent kinases
Authors: Bettayeb, K. / Tirado, O.M. / Marionneau-Lambot, S. / Ferandin, Y. / Lozach, O. / Morris, J.C. / Mateo-Lozano, S. / Drueckes, P. / Kubbutat, M.H. / Liger, F. / Marquet, B. / Joseph, B. / ...Authors: Bettayeb, K. / Tirado, O.M. / Marionneau-Lambot, S. / Ferandin, Y. / Lozach, O. / Morris, J.C. / Mateo-Lozano, S. / Drueckes, P. / Kubbutat, M.H. / Liger, F. / Marquet, B. / Joseph, B. / Echalier, A. / Endicott, J.A. / Notario, V. / Meijer, L.
History
DepositionNov 29, 2007Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 12, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 25, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / struct_conn / struct_conn_type / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn_type.id / _struct_ref_seq_dif.details / _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: 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)129,0268
Polymers128,4384
Non-polymers5874
Water8,899494
1
A: Cell division protein kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5134
Polymers64,2192
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3630 Å2
MethodPISA
2
C: Cell division protein kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5134
Polymers64,2192
Non-polymers2942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3740 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.146, 133.957, 147.837
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cell division protein kinase 2 / p33 protein kinase / CDK2


Mass: 34200.602 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2 / Plasmid: pGEX / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A


Mass: 30018.631 Da / Num. of mol.: 2 / Fragment: UNP residues 169-430
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (cattle) / Gene: CCNA2, CCNA / Plasmid: pET / Production host: Escherichia coli (E. coli) / Strain (production host): B834 / References: UniProt: P30274
#3: Chemical ChemComp-MHR / 4-(4-propoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine


Mass: 269.302 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C14H15N5O
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.86 Å3/Da / Density % sol: 56.96 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7
Details: ammonium sulphate, potassium chloride, HEPES pH7.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jul 1, 2007
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. obs: 65608 / % possible obs: 99.3 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.087 / Net I/σ(I): 11.1
Reflection shellResolution: 2.3→2.42 Å / Rmerge(I) obs: 0.439 / Mean I/σ(I) obs: 3 / % possible all: 98.3

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
MAR345data collection
MOLREPphasing
RefinementResolution: 2.3→20 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.906 / SU B: 10.687 / SU ML: 0.156 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.283 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.24 3322 5.1 %RANDOM
Rwork0.194 ---
obs0.197 65469 99.15 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 10.456 Å2
Baniso -1Baniso -2Baniso -3
1-0.15 Å20 Å20 Å2
2---0.92 Å20 Å2
3---0.76 Å2
Refinement stepCycle: LAST / Resolution: 2.3→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8797 0 42 494 9333
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0229158
X-RAY DIFFRACTIONr_angle_refined_deg1.3161.98312457
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.56151117
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.95824.099405
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.525151616
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.0871546
X-RAY DIFFRACTIONr_chiral_restr0.0970.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026841
X-RAY DIFFRACTIONr_nbd_refined0.1860.24465
X-RAY DIFFRACTIONr_nbtor_refined0.2980.26249
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2534
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1560.252
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2950.225
X-RAY DIFFRACTIONr_mcbond_it0.4491.55693
X-RAY DIFFRACTIONr_mcangle_it0.79228980
X-RAY DIFFRACTIONr_scbond_it1.03333937
X-RAY DIFFRACTIONr_scangle_it1.6564.53463
LS refinement shellResolution: 2.3→2.359 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.298 262 -
Rwork0.256 4370 -
all-4632 -
obs--97.64 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.25620.08440.36471.0671-0.05661.43380.0178-0.002-0.0215-0.1539-0.0166-0.14530.15640.1058-0.0012-0.21310.01910.0243-0.0651-0.0101-0.2005-8.87623.474-12.224
21.1666-0.2416-0.29041.66380.28051.68220.0062-0.1308-0.08790.020.06940.00220.31940.0005-0.0756-0.1357-0.0153-0.0337-0.040.0625-0.191-21.151-0.9142.449
31.06690.48480.51721.90460.21881.04340.05840.043-0.04390.1445-0.05960.05590.1004-0.13140.00120.0001-0.00680.0423-0.0291-0.0288-0.1734-42.886-12.771-31.232
41.62540.3754-0.04892.39360.16491.7989-0.0520.0580.25190.1494-0.03650.4747-0.1839-0.26140.08850.01260.10590.0239-0.0656-0.0284-0.096-44.5218.011-33.924
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA10 - 20012 - 202
2X-RAY DIFFRACTION1AA260 - 280262 - 282
3X-RAY DIFFRACTION2BB180 - 42010 - 250
4X-RAY DIFFRACTION3CC10 - 20012 - 202
5X-RAY DIFFRACTION3CC260 - 280262 - 282
6X-RAY DIFFRACTION4DD180 - 42010 - 250

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