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- PDB-8fp5: CDK2 liganded with ATP and Mg2+ -

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Basic information

Entry
Database: PDB / ID: 8fp5
TitleCDK2 liganded with ATP and Mg2+
ComponentsCyclin-dependent kinase 2
KeywordsCell Cycle / Transferase / allosteric / inhibitor
Function / homology
Function and homology information


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 ...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 / Defective binding of RB1 mutants to E2F1,(E2F2, E2F3) / centriole replication / Regulation of APC/C activators between G1/S and early anaphase / centrosome duplication / Telomere Extension By Telomerase / G0 and Early G1 / Activation of the pre-replicative complex / cellular response to nitric oxide / cyclin-dependent protein kinase holoenzyme complex / cyclin-dependent kinase / cyclin-dependent protein serine/threonine kinase activity / TP53 Regulates Transcription of Genes Involved in G1 Cell Cycle Arrest / 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 / Cajal body / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of mitotic cell cycle / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / : / meiotic cell cycle / positive regulation of DNA replication / male germ cell nucleus / 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 / Orc1 removal from chromatin / G1/S transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / 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 / DNA replication / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / endosome / chromatin remodeling / protein domain specific binding / cell division / protein phosphorylation / DNA repair / protein serine kinase activity / 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 / cytoplasm / cytosol
Similarity search - Function
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
ADENOSINE-5'-TRIPHOSPHATE / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsSchonbrunn, E. / Sun, L.
Funding support United States, 1items
OrganizationGrant numberCountry
Not funded United States
CitationJournal: Nat Commun / Year: 2023
Title: Development of allosteric and selective CDK2 inhibitors for contraception with negative cooperativity to cyclin binding.
Authors: Faber, E.B. / Sun, L. / Tang, J. / Roberts, E. / Ganeshkumar, S. / Wang, N. / Rasmussen, D. / Majumdar, A. / Hirsch, L.E. / John, K. / Yang, A. / Khalid, H. / Hawkinson, J.E. / Levinson, N.M. ...Authors: Faber, E.B. / Sun, L. / Tang, J. / Roberts, E. / Ganeshkumar, S. / Wang, N. / Rasmussen, D. / Majumdar, A. / Hirsch, L.E. / John, K. / Yang, A. / Khalid, H. / Hawkinson, J.E. / Levinson, N.M. / Chennathukuzhi, V. / Harki, D.A. / Schonbrunn, E. / Georg, G.I.
History
DepositionJan 4, 2023Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 31, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 14, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year
Revision 1.2Oct 25, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cyclin-dependent kinase 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,5704
Polymers33,9761
Non-polymers5943
Water2,630146
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.670, 71.710, 72.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CDK2, CDKN2 / Plasmid: pGEX6P1 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 DE3 RIPL / References: UniProt: P24941, cyclin-dependent kinase
#2: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION / Comment: ATP, energy-carrying molecule*YM
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 146 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.04 Å3/Da / Density % sol: 39.71 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 10% PEG 3350, 10% ethylene glycol, 50mM HEPES, pH 7.5

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Data collection

DiffractionMean temperature: 93 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 / Wavelength: 1.5418 Å
DetectorType: RIGAKU SATURN 944+ / Detector: CCD / Date: Nov 20, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.7→27.6 Å / Num. obs: 31044 / % possible obs: 99.3 % / Redundancy: 3.6 % / Biso Wilson estimate: 23.2 Å2 / CC1/2: 1 / Rrim(I) all: 0.035 / Net I/σ(I): 23.7
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 2.7 % / Mean I/σ(I) obs: 1.3 / Num. unique obs: 2197 / CC1/2: 0.55 / Rrim(I) all: 1.04 / % possible all: 96.5

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Processing

Software
NameVersionClassification
PHENIX1.20.1-4487refinement
XDSJan 10, 2022data reduction
XSCALEJan 10, 2022data scaling
PHENIX1.20.1-4487phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1B39

1b39


Resolution: 1.7→27.6 Å / SU ML: 0.21 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 23.84 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2304 1553 5 %
Rwork0.1942 --
obs0.196 31042 99.31 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.7→27.6 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2314 0 36 146 2496
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.009
X-RAY DIFFRACTIONf_angle_d1.184
X-RAY DIFFRACTIONf_dihedral_angle_d7.849323
X-RAY DIFFRACTIONf_chiral_restr0.073372
X-RAY DIFFRACTIONf_plane_restr0.01418
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.7-1.750.33761350.28582559X-RAY DIFFRACTION97
1.75-1.820.27861370.24712610X-RAY DIFFRACTION98
1.82-1.890.26591390.25022638X-RAY DIFFRACTION99
1.89-1.980.24391400.20712646X-RAY DIFFRACTION99
1.98-2.080.20921400.19472675X-RAY DIFFRACTION100
2.08-2.210.21411410.19282666X-RAY DIFFRACTION100
2.21-2.380.21431410.19042680X-RAY DIFFRACTION100
2.38-2.620.22861410.20032689X-RAY DIFFRACTION100
2.62-30.26851440.2062724X-RAY DIFFRACTION100
3-3.780.24541440.18632736X-RAY DIFFRACTION100
3.78-27.60.19611510.17152866X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -1.7951 Å / Origin y: -5.4934 Å / Origin z: 14.053 Å
111213212223313233
T0.1564 Å2-0.0004 Å2-0.0096 Å2-0.1415 Å2-0.0043 Å2--0.1862 Å2
L0.9058 °2-0.1428 °2-0.0419 °2-0.7914 °20.4338 °2--2.1886 °2
S0.0091 Å °-0.1324 Å °0.0119 Å °0.1118 Å °0.028 Å °-0.1157 Å °0.0758 Å °0.11 Å °-0.0422 Å °
Refinement TLS groupSelection details: all

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