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- PDB-9esv: CDK2-cyclin A in complex with FragLite 19 -

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Basic information

Entry
Database: PDB / ID: 9esv
TitleCDK2-cyclin A in complex with FragLite 19
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) / microtubule organizing center / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / 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 / 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-bromo-2-methoxyphenol / Cyclin-dependent kinase 2 / Cyclin-A2
Similarity search - Component
Biological speciesHomo sapiens (human)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.397 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 1.0Sep 3, 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)132,17213
Polymers130,3444
Non-polymers1,8279
Water4,035224
1
A: Cyclin-dependent kinase 2
B: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)66,3908
Polymers65,1722
Non-polymers1,2186
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3680 Å2
ΔGint-15 kcal/mol
Surface area23220 Å2
MethodPISA
2
C: Cyclin-dependent kinase 2
D: Cyclin-A2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)65,7815
Polymers65,1722
Non-polymers6093
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3600 Å2
ΔGint-16 kcal/mol
Surface area22070 Å2
MethodPISA
Unit cell
Length a, b, c (Å)74.016, 133.921, 147.886
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-3Z7 / 4-bromo-2-methoxyphenol


Mass: 203.033 Da / Num. of mol.: 9 / Source method: obtained synthetically / Formula: C7H7BrO2 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 224 / 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: 56.25 %
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: 2.37→147.89 Å / Num. obs: 59941 / % possible obs: 99 % / Redundancy: 13.7 % / CC1/2: 0.995 / Rmerge(I) obs: 0.373 / Rpim(I) all: 0.15 / Rrim(I) all: 0.402 / Net I/σ(I): 6.6
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rpim(I) allRrim(I) all% possible all
10.33-147.8912.20.05928.38550.9990.0230.06399.9
2.38-2.4313.24.9650.646740.1842.0515.375100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2data reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.397→99.465 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.943 / WRfactor Rfree: 0.232 / WRfactor Rwork: 0.217 / Average fsc free: 0.9245 / Average fsc work: 0.9281 / Cross valid method: THROUGHOUT / ESU R: 0.409 / ESU R Free: 0.233 / Details: Hydrogens have not been used
RfactorNum. reflection% reflection
Rfree0.229 2911 5.133 %
Rwork0.2271 53805 -
all0.227 --
obs-56716 97.005 %
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: 66.299 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å2-0 Å20 Å2
2--0.124 Å2-0 Å2
3----0.184 Å2
Refinement stepCycle: LAST / Resolution: 2.397→99.465 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8771 0 90 224 9085
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0129156
X-RAY DIFFRACTIONr_angle_refined_deg1.591.84112437
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.80451096
X-RAY DIFFRACTIONr_dihedral_angle_2_deg27.534556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.281101590
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.66410394
X-RAY DIFFRACTIONr_chiral_restr0.1060.21399
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026858
X-RAY DIFFRACTIONr_nbd_refined0.2320.24610
X-RAY DIFFRACTIONr_nbtor_refined0.3190.26230
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1380.2403
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.240.249
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.2370.27
X-RAY DIFFRACTIONr_mcbond_it4.6676.4364384
X-RAY DIFFRACTIONr_mcangle_it7.29711.5675480
X-RAY DIFFRACTIONr_scbond_it6.0456.774772
X-RAY DIFFRACTIONr_scangle_it9.20412.2856957
X-RAY DIFFRACTIONr_lrange_it12.92869.81314308
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
2.397-2.4591.1081491.11630121.11542810.7190.77473.83791.105
2.459-2.5270.7572470.75438800.75441270.7520.7441000.784
2.527-2.60.4632030.47638350.47540390.8660.85899.97520.474
2.6-2.680.3432060.34537380.34539440.910.9151000.35
2.68-2.7680.2931880.31336140.31238020.9430.931000.314
2.768-2.8650.2681730.28435280.28337010.9570.9431000.282
2.865-2.9730.3172110.27633580.27835690.9380.9471000.272
2.973-3.0940.2851720.26432730.26534450.9560.9581000.256
3.094-3.2320.2261650.24831360.24733010.9710.9641000.238
3.232-3.3890.231530.23530200.23531730.9690.9691000.224
3.389-3.5720.2111290.20522670.20630110.9790.97679.57490.196
3.572-3.7890.1791530.18626930.18528460.9810.981000.176
3.789-4.050.1621250.16925730.16926980.9840.9831000.16
4.05-4.3740.1561400.15223990.15225390.9860.9861000.146
4.374-4.790.151190.14621950.14623140.9850.9871000.142
4.79-5.3540.177960.17920290.17921250.9840.9831000.176
5.354-6.1790.196980.21217950.21118930.9820.9811000.207
6.179-7.5610.2920.20715150.20716070.9770.9811000.208
7.561-10.6620.156560.15712200.15712760.9860.9871000.17
10.662-99.4650.314360.2437250.2457620.8550.96399.86880.279

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