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- PDB-9esl: CDK2-cyclin A in complex with FragLite 29 -

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Basic information

Entry
Database: PDB / ID: 9esl
TitleCDK2-cyclin A in complex with FragLite 29
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 / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity ...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 / G2 Phase / Y chromosome / cyclin-dependent protein kinase activity / 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 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / microtubule organizing center / regulation of DNA replication / telomere maintenance in response to DNA damage / centrosome duplication / G0 and Early G1 / Telomere Extension By Telomerase / 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 / Cajal body / Activation of ATR in response to replication stress / Cyclin E associated events during G1/S transition / Cyclin A/B1/B2 associated events during G2/M transition / Cyclin A:Cdk2-associated events at S phase entry / cyclin-dependent protein kinase holoenzyme complex / condensed chromosome / regulation of G2/M transition of mitotic cell cycle / mitotic G1 DNA damage checkpoint signaling / cellular response to nitric oxide / post-translational protein modification / cyclin binding / regulation of mitotic cell cycle / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / DNA Damage/Telomere Stress Induced Senescence / potassium ion transport / CDK-mediated phosphorylation and removal of Cdc6 / Meiotic recombination / SCF(Skp2)-mediated degradation of p27/p21 / G2/M transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / Orc1 removal from chromatin / 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 / Senescence-Associated Secretory Phenotype (SASP) / transcription regulator complex / Regulation of TP53 Activity through Phosphorylation / Ras protein signal transduction / chromosome, telomeric region / DNA replication / protein phosphorylation / endosome / chromatin remodeling / protein domain specific binding / cell division / protein serine kinase activity / DNA repair / protein serine/threonine kinase activity / positive regulation of cell population proliferation / DNA-templated transcription / centrosome / positive regulation of DNA-templated transcription / magnesium ion binding / negative regulation of transcription by RNA polymerase II / signal transduction / nucleoplasm / ATP binding / nucleus / cytoplasm / cytosol
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-(2-methoxyethyl)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: 2.392 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: Structure / Year: 2025
Title: Crystallographic fragment screening of CDK2-cyclin A: FragLites map sites of protein-protein interaction.
Authors: Hope, I. / Martin, M.P. / Jiang, Z. / 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
Revision 1.1Aug 27, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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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)131,96911
Polymers130,3444
Non-polymers1,6257
Water6,233346
1
A: Cyclin-dependent kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,1016
Polymers65,1722
Non-polymers9284
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3560 Å2
ΔGint-15 kcal/mol
Surface area23550 Å2
MethodPISA
2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,8685
Polymers65,1722
Non-polymers6963
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-15 kcal/mol
Surface area22120 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.132, 134.211, 147.853
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: PET21d / 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-V3U / 4-bromanyl-1-(2-methoxyethyl)pyridin-2-one


Mass: 232.074 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C8H10BrNO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 346 / 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: 2.82 Å3/Da / Density % sol: 56.41 %
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: 0.89842 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: 0.89842 Å / Relative weight: 1
ReflectionResolution: 2.38→134.21 Å / Num. obs: 58464 / % possible obs: 97.5 % / Redundancy: 13.7 % / CC1/2: 0.999 / Rmerge(I) obs: 0.12 / Rpim(I) all: 0.048 / Rrim(I) all: 0.129 / Net I/σ(I): 13.2
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
10.37-134.21120.02949.484110.0110.03199.8
2.38-2.4513.51.3511.745780.7590.5511.461100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.392→99.573 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.942 / WRfactor Rfree: 0.22 / WRfactor Rwork: 0.205 / Average fsc free: 0.9579 / Average fsc work: 0.9574 / Cross valid method: THROUGHOUT / ESU R: 0.395 / ESU R Free: 0.225 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.2203 2893 5.075 %
Rwork0.2166 54117 -
all0.217 --
obs-57010 96.531 %
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: 65.194 Å2
Baniso -1Baniso -2Baniso -3
1--1.866 Å20 Å20 Å2
2--1.165 Å20 Å2
3---0.701 Å2
Refinement stepCycle: LAST / Resolution: 2.392→99.573 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8791 0 84 346 9221
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129162
X-RAY DIFFRACTIONr_angle_refined_deg1.5091.84812440
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.08351099
X-RAY DIFFRACTIONr_dihedral_angle_2_deg25.507545
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.257101593
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.83610395
X-RAY DIFFRACTIONr_chiral_restr0.0740.21402
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026845
X-RAY DIFFRACTIONr_nbd_refined0.2250.24419
X-RAY DIFFRACTIONr_nbtor_refined0.3160.26261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1610.2443
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3010.253
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2980.211
X-RAY DIFFRACTIONr_mcbond_it3.9256.2214396
X-RAY DIFFRACTIONr_mcangle_it5.86511.1775495
X-RAY DIFFRACTIONr_scbond_it4.9656.7534766
X-RAY DIFFRACTIONr_scangle_it7.64312.2116945
X-RAY DIFFRACTIONr_lrange_it11.11568.84914159
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
2.392-2.4541.2441531.24335791.24342540.850.83787.72921.465
2.454-2.5210.4082390.41739740.41742130.9240.9271000.423
2.521-2.5940.3082220.29238810.29341030.9440.9521000.286
2.594-2.6740.2392050.2537600.2539650.9610.961000.24
2.674-2.7610.2461890.24836580.24838470.9620.961000.235
2.761-2.8580.2381800.25135840.2537640.9680.961000.238
2.858-2.9660.2611990.24333920.24435910.9580.9631000.229
2.966-3.0870.2551830.2433000.2434830.9620.9661000.227
3.087-3.2240.2211670.23331840.23333510.9730.9661000.221
3.224-3.3810.2331530.22130370.22231900.9680.9711000.211
3.381-3.5640.1731260.20222820.20130360.9860.97779.31490.194
3.564-3.780.1881330.19322500.19328820.9820.97982.68560.188
3.78-4.040.2091010.18822410.18927220.9780.9886.03970.181
4.04-4.3630.1651400.16624300.16525700.9880.9851000.161
4.363-4.7790.1711230.15722170.15823400.9830.9861000.154
4.779-5.3420.175940.17520500.17521440.980.9821000.171
5.342-6.1650.2281010.21218000.21319010.9740.9761000.208
6.165-7.5430.238910.21815330.21916240.9660.9761000.216
7.543-10.6370.162570.15112350.15112920.9850.9871000.155
10.637-99.5730.278370.2467300.2477690.8930.96299.73990.267

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