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

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Basic information

Entry
Database: PDB / ID: 3bht
TitleStructure of phosphorylated Thr160 CDK2/cyclin A in complex with the inhibitor meriolin 3
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-MFR / MONOTHIOGLYCEROL / Cyclin-dependent kinase 2 / Cyclin-A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2 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 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)129,29411
Polymers128,4384
Non-polymers8567
Water19,4201078
1
A: Cell division protein kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,7016
Polymers64,2192
Non-polymers4824
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4130 Å2
MethodPISA
2
C: Cell division protein kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,5935
Polymers64,2192
Non-polymers3743
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.128, 133.770, 147.831
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 2 types, 4 molecules ACBD

#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

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Non-polymers , 4 types, 1085 molecules

#3: Chemical ChemComp-MFR / 4-(4-methoxy-1H-pyrrolo[2,3-b]pyridin-3-yl)pyrimidin-2-amine


Mass: 241.249 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C12H11N5O
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#5: Chemical ChemComp-SGM / MONOTHIOGLYCEROL


Mass: 108.159 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C3H8O2S
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1078 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.85 Å3/Da / Density % sol: 56.89 %
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: ESRF / Beamline: ID14-2 / Wavelength: 0.933 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 29, 2006
RadiationMonochromator: Si 111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 95411 / % possible obs: 95.5 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Rmerge(I) obs: 0.051 / Net I/σ(I): 16.3
Reflection shellResolution: 2→2.11 Å / Rmerge(I) obs: 0.225 / Mean I/σ(I) obs: 4.8 / % possible all: 77

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALAdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT3.004data extraction
ADSCQuantumdata collection
MOLREPphasing
RefinementResolution: 2→20 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.93 / SU B: 5.802 / SU ML: 0.097 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.167 / ESU R Free: 0.151 / Stereochemistry target values: MAXIMUM LIKELIHOOD
RfactorNum. reflection% reflectionSelection details
Rfree0.22 4777 5 %RANDOM
Rwork0.181 ---
obs0.183 95266 95.52 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 9.6 Å2
Baniso -1Baniso -2Baniso -3
1-0.32 Å20 Å20 Å2
2---1.17 Å20 Å2
3---0.85 Å2
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8793 0 56 1078 9927
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0229154
X-RAY DIFFRACTIONr_angle_refined_deg1.3651.98412441
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.95351111
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.55924.025400
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.165151605
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.9821546
X-RAY DIFFRACTIONr_chiral_restr0.1170.21412
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026817
X-RAY DIFFRACTIONr_nbd_refined0.1990.24595
X-RAY DIFFRACTIONr_nbtor_refined0.3040.26245
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1730.2899
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2070.265
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.160.241
X-RAY DIFFRACTIONr_mcbond_it0.6451.55715
X-RAY DIFFRACTIONr_mcangle_it1.09328976
X-RAY DIFFRACTIONr_scbond_it1.65433938
X-RAY DIFFRACTIONr_scangle_it2.5284.53455
LS refinement shellResolution: 2→2.051 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.248 262 -
Rwork0.207 4838 -
all-5100 -
obs--70.78 %
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)
11.07130.06010.31570.9633-0.05851.24240.00810.0226-0.0179-0.14720.0049-0.1210.12010.0982-0.013-0.23640.01650.0273-0.0631-0.0072-0.1653-8.87623.474-12.224
21.0178-0.1631-0.25551.50930.06731.3632-0.0081-0.1319-0.1149-0.0080.0640.01530.29890.0035-0.056-0.1418-0.0112-0.0386-0.04080.053-0.1577-21.151-0.9142.449
30.88920.40910.33821.91440.19030.83470.05560.0122-0.00940.1852-0.05190.10740.0839-0.0915-0.00360.00050.00440.054-0.0503-0.0262-0.1479-42.886-12.771-31.232
41.57570.4338-0.252.51960.18951.457-0.01830.04830.260.1951-0.0310.5297-0.2088-0.19060.0492-0.00010.09730.0444-0.0796-0.0234-0.0485-44.5218.011-33.924
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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