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- PDB-1aq1: HUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR STAU... -

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Basic information

Entry
Database: PDB / ID: 1aq1
TitleHUMAN CYCLIN DEPENDENT KINASE 2 COMPLEXED WITH THE INHIBITOR STAUROSPORINE
ComponentsCYCLIN-DEPENDENT PROTEIN KINASE 2
KeywordsPROTEIN KINASE / CELL CYCLE / PHOSPHORYLATION / STAUROSPORINE / CELL DIVISION / MITOSIS / INHIBITION
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 / 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 ...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 / 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 / Activation of ATR in response to replication stress / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / Cajal body / Cyclin E associated events during G1/S transition / Cyclin A:Cdk2-associated events at S phase entry / Cyclin A/B1/B2 associated events during G2/M transition / 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 / regulation of mitotic cell cycle / cyclin binding / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / G1/S transition of mitotic cell cycle / peptidyl-serine phosphorylation / 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 / 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 / DNA replication / chromosome, telomeric region / 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
: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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 ...: / Phosphorylase Kinase; domain 1 / Phosphorylase Kinase; domain 1 / Transferase(Phosphotransferase) domain 1 / Transferase(Phosphotransferase); 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
STAUROSPORINE / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / DIFFERENCE FOURIER / Resolution: 2 Å
AuthorsEndicott, J.A. / Noble, M.E.M. / Johnson, L.N. / Lawrie, A. / Tunnah, P. / Brown, N.R.
Citation
Journal: Nat.Struct.Biol. / Year: 1997
Title: Protein kinase inhibition by staurosporine revealed in details of the molecular interaction with CDK2.
Authors: Lawrie, A.M. / Noble, M.E. / Tunnah, P. / Brown, N.R. / Johnson, L.N. / Endicott, J.A.
#1: Journal: Nature / Year: 1993
Title: Crystal Structure of Cyclin-Dependent Kinase 2
Authors: De Bondt, H.L. / Rosenblatt, J. / Jancarik, J. / Jones, H.D. / Morgan, D.O. / Kim, S.H.
History
DepositionAug 5, 1997Processing site: BNL
Revision 1.0Nov 12, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 3, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 2, 2023Group: Database references / Derived calculations ...Database references / Derived calculations / Other / Refinement description
Category: database_2 / pdbx_database_status ...database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.process_site / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4May 22, 2024Group: 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 PROTEIN KINASE 2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4432
Polymers33,9761
Non-polymers4671
Water2,252125
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)53.500, 70.500, 73.600
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 PROTEIN KINASE 2 / CDK2


Mass: 33976.488 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: COMPLEX WITH CYCLIN A OR CYCLIN E / Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Cell line (production host): SF9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P24941, EC: 2.7.1.37
#2: Chemical ChemComp-STU / STAUROSPORINE


Mass: 466.531 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H26N4O3 / Comment: antibiotic*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 125 / Source method: isolated from a natural source / Formula: H2O

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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 Å3/Da / Density % sol: 32 %
Crystal growMethod: vapor diffusion / pH: 7.4
Details: PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. ...Details: PROTEIN AT 10MG/ML IN 15MM NACL, 10MM HEPES, PH7.4, MIXED WITH WELL BUFFER (50MM AMMONIUM ACETATE, 10% PEG4K, 0.1M HEPES PH 7.4) IN EQUAL VOLUMES, THEN VAPOUR DIFFUSION AGAINST WELL BUFFER. CDK2 CRYSTALS WERE SOAKED FOR 20 HOURS IN A SOLUTION OF 0.5MM STAUROSPORINE IN 1X WELL BUFFER PREPARED FROM STOCKS 2X WELLBUFFER AND 10MM STAUROSPORINE IN 100% DMSO., vapor diffusion
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, sitting drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlCDK21drop
215 mM1dropNaCl
310 mMHEPES1drop
450 mM1reservoirNH4Ac
510 %PEG40001reservoir
60.1 MHEPES1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 0.9
DetectorType: MARRESEARCH / Detector: IMAGE PLATE AREA DETECTOR / Date: Dec 1, 1996 / Details: MIRROR
RadiationMonochromator: TWIN CRYSTAL / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9 Å / Relative weight: 1
ReflectionResolution: 2→20 Å / Num. obs: 17731 / % possible obs: 92.9 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 5.7
Reflection shellResolution: 2→2.1 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.5 / Mean I/σ(I) obs: 1.4 / % possible all: 89.4
Reflection
*PLUS
Highest resolution: 2 Å / Num. measured all: 53349 / Rmerge(I) obs: 0.101
Reflection shell
*PLUS
Highest resolution: 2 Å / Lowest resolution: 2.11 Å

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Processing

Software
NameVersionClassification
CCP4model building
REFMACrefinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
CCP4phasing
RefinementMethod to determine structure: DIFFERENCE FOURIER
Starting model: PDB ENTRY 1HCK

1hck


Resolution: 2→25 Å / Cross valid method: FREE-R / σ(F): 0
Details: REFINEMENT BEGUN WITH X-PLOR RIGID BODY REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.26 919 5 %RANDOM
Rwork0.22 ---
obs-17721 92.9 %-
Refinement stepCycle: LAST / Resolution: 2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2230 0 35 125 2390
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Num. reflection all: 17721 / Rfactor all: 0.22
Solvent computation
*PLUS
Displacement parameters
*PLUS

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