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- PDB-9et7: CDK2-cyclin A in complex with FragLite 6 -

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Basic information

Entry
Database: PDB / ID: 9et7
TitleCDK2-cyclin A in complex with FragLite 6
Components
  • Cyclin-A2
  • Cyclin-dependent kinase 2
KeywordsCELL CYCLE / cyclin-dependent kinase / FragLite / CDK2 / cyclin A / Fragment
Function / homology
Function and homology information


cell cycle G1/S 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 / cyclin-dependent protein kinase activity / G2 Phase / Y chromosome ...cell cycle G1/S 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 / cyclin-dependent protein kinase activity / G2 Phase / 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 / microtubule organizing center / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / regulation of DNA 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 / 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 / Cajal body / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cellular response to nitric oxide / post-translational protein modification / cyclin binding / male germ cell nucleus / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / 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 / regulation of gene expression / peptidyl-serine phosphorylation / Senescence-Associated Secretory Phenotype (SASP) / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / DNA replication / chromosome, telomeric region / endosome / protein phosphorylation / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / DNA-templated transcription / centrosome / 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, N-terminal ...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, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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
Similarity search - Domain/homology
4-bromanyl-1~{H}-pyridin-2-one / Cyclin-dependent kinase 2 / Cyclin-A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.312 Å
AuthorsHope, I. / Martin, M.P. / Waring, M.J. / Noble, M.E.M. / Endicott, J.A. / Tatum, N.J.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Medical Research Council (MRC, United Kingdom)MR/N009738/1 United Kingdom
Medical Research Council (MRC, United Kingdom)MR/V029142/1 United Kingdom
Cancer Research UKC2115/A21421 United Kingdom
CitationJournal: To Be Published
Title: Crystallographic fragment screening of CDK2-cyclin A: FragLites map sites of protein-protein interaction
Authors: Hope, I. / Martin, M.P. / Waring, M.J. / Noble, M.E.M. / Endicott, J.A. / Tatum, N.J.
History
DepositionMar 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 9, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
B: Cyclin-A2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)130,8667
Polymers130,3444
Non-polymers5223
Water5,170287
1
A: Cyclin-dependent kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,5204
Polymers65,1722
Non-polymers3482
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3530 Å2
ΔGint-16 kcal/mol
Surface area23130 Å2
MethodPISA
2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,3463
Polymers65,1722
Non-polymers1741
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-18 kcal/mol
Surface area23180 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.181, 133.725, 147.94
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Cyclin-dependent kinase 2 / Cell division protein kinase 2 / p33 protein kinase


Mass: 34354.770 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: PGEX6P1 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P24941, cyclin-dependent kinase
#2: Protein Cyclin-A2 / Cyclin-A


Mass: 30817.473 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Gene: CCNA2 / Plasmid: PET21d / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P30274
#3: Chemical ChemComp-HGQ / 4-bromanyl-1~{H}-pyridin-2-one


Mass: 173.995 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C5H4BrNO / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
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: 2.81 Å3/Da / Density % sol: 56.3 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7
Details: Protein at 10 mg/ml. 0.6 to 0.8 M KCl, 0.9 to 1.2 M (NH4)2SO4, and 100 mM HEPES pH 7.0
PH range: 7-7.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.89843620172867 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 9, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.89843620172867 Å / Relative weight: 1
ReflectionResolution: 2.3→147.94 Å / Num. obs: 62435 / % possible obs: 94.3 % / Redundancy: 13.5 % / CC1/2: 0.999 / Rmerge(I) obs: 0.136 / Net I/σ(I): 12.3
Reflection shellResolution: 2.3→2.36 Å / Redundancy: 13.4 % / Rmerge(I) obs: 1.4 / Mean I/σ(I) obs: 1.8 / Num. unique obs: 4816 / CC1/2: 0.71 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.312→99.401 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.938 / WRfactor Rfree: 0.251 / WRfactor Rwork: 0.225 / Average fsc free: 0.925 / Average fsc work: 0.9384 / Cross valid method: THROUGHOUT / ESU R: 0.393 / ESU R Free: 0.264 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2713 3100 5.12 %
Rwork0.2394 57449 -
all0.241 --
obs-60549 93.016 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 36.291 Å2
Baniso -1Baniso -2Baniso -3
1--1.975 Å20 Å20 Å2
2--1.573 Å20 Å2
3---0.402 Å2
Refinement stepCycle: LAST / Resolution: 2.312→99.401 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8960 0 24 287 9271
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0129274
X-RAY DIFFRACTIONr_angle_refined_deg1.4681.84612609
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.74851122
X-RAY DIFFRACTIONr_dihedral_angle_2_deg24.432545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.506101617
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.6110404
X-RAY DIFFRACTIONr_chiral_restr0.0680.21423
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026984
X-RAY DIFFRACTIONr_nbd_refined0.210.24169
X-RAY DIFFRACTIONr_nbtor_refined0.310.26425
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2380
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2340.257
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.220.215
X-RAY DIFFRACTIONr_mcbond_it2.4883.3984482
X-RAY DIFFRACTIONr_mcangle_it3.9056.115606
X-RAY DIFFRACTIONr_scbond_it3.0343.7164792
X-RAY DIFFRACTIONr_scangle_it4.876.6977003
X-RAY DIFFRACTIONr_lrange_it7.84238.23713992
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
2.312-2.3731.4652061.42237571.42447160.760.74984.03311.561
2.373-2.4380.5782510.53143890.53446400.8570.8611000.553
2.438-2.5080.4342410.3742630.37445040.9110.9311000.372
2.508-2.5850.3442350.29141520.29343870.9140.9441000.286
2.585-2.670.2881930.2832740.28142660.9390.9581.27050.273
2.67-2.7640.3321730.2831930.28341110.9340.94981.87790.268
2.764-2.8680.3291840.27737690.27939530.9290.9511000.263
2.868-2.9850.3021860.27536580.27638440.9380.9521000.261
2.985-3.1170.3421810.2735100.27336910.9310.9551000.257
3.117-3.2690.271840.26133290.26135130.9560.961000.248
3.269-3.4460.2871670.24427600.24633520.9450.96587.3210.235
3.446-3.6550.3191070.22623590.2331830.9380.97177.47410.219
3.655-3.9070.224990.20419680.20530170.9680.97668.51180.198
3.907-4.2190.2151310.19525130.19627790.970.97995.14210.191
4.219-4.6210.1771390.1824800.1826190.9810.9821000.178
4.621-5.1650.2261230.1822120.18223350.970.981000.178
5.165-5.9620.2241110.21119850.21220960.9750.9761000.206
5.962-7.2950.262850.21317180.21518030.9620.9771000.208
7.295-10.2890.179710.15113510.15314220.9830.9871000.157
10.289-99.4010.192330.2078090.2068440.9820.96899.7630.24

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