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- PDB-1e9h: Thr 160 phosphorylated CDK2 - Human cyclin A3 complex with the in... -

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Basic information

Entry
Database: PDB / ID: 1e9h
TitleThr 160 phosphorylated CDK2 - Human cyclin A3 complex with the inhibitor indirubin-5-sulphonate bound
Components
  • CELL DIVISION PROTEIN KINASE 2
  • CYCLIN A3
KeywordsCELL CYCLE / COMPLEX (PROTEIN KINASE-CYCLIN) / KINASES / INHIBITOR / CYCLIN / COMPLEX / PHOSPHORYLATION
Function / homology
Function and homology information


: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon ...: / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / Transcription of E2F targets under negative control by p107 (RBL1) and p130 (RBL2) in complex with HDAC1 / cellular response to leptin stimulus / male pronucleus / female pronucleus / cellular response to cocaine / response to glucagon / cyclin-dependent protein serine/threonine kinase regulator activity / positive regulation of DNA biosynthetic process / cellular response to insulin-like growth factor stimulus / 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 / 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 / telomere maintenance in response to DNA damage / regulation of DNA replication / centrosome duplication / G0 and Early G1 / cochlea development / Telomere Extension By Telomerase / animal organ regeneration / 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 / cellular response to platelet-derived growth factor stimulus / 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 / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / positive regulation of DNA replication / meiotic cell cycle / male germ cell nucleus / cellular response to estradiol stimulus / CDK-mediated phosphorylation and removal of Cdc6 / G1/S transition of mitotic cell cycle / SCF(Skp2)-mediated degradation of p27/p21 / peptidyl-serine phosphorylation / DNA Damage/Telomere Stress Induced Senescence / Orc1 removal from chromatin / potassium ion transport / Meiotic recombination / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / Transcriptional regulation of granulopoiesis / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / cellular senescence / nuclear envelope / Processing of DNA double-strand break ends / regulation of gene expression / Senescence-Associated Secretory Phenotype (SASP) / Factors involved in megakaryocyte development and platelet production / Regulation of TP53 Activity through Phosphorylation / cellular response to hypoxia / transcription regulator complex / Ras protein signal transduction / chromosome, telomeric region / DNA replication / protein phosphorylation / Ub-specific processing proteases / 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 / protein kinase binding
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-like / Cyclin, C-terminal domain / Cyclin_C ...Cyclin-A, N-terminal APC/C binding region / Cyclin-A N-terminal APC/C binding region / : / Cyclin, C-terminal domain / : / Cyclins signature. / Cyclin / Cyclin-like / Cyclin, C-terminal domain / Cyclin_C / Cyclin A; domain 1 / Cyclin, N-terminal / Cyclin, N-terminal domain / Cyclin-like / domain present in cyclins, TFIIB and Retinoblastoma / Cyclin-like superfamily / : / 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
Chem-INR / Cyclin-A2 / Cyclin-dependent kinase 2
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDavies, T.G. / Tunnah, P. / Noble, M.E.M. / Endicott, J.A.
CitationJournal: Structure / Year: 2001
Title: Inhibitor Binding to Active and Inactive Cdk2: The Crystal Structure of Cdk2-Cyclin A/Indirubin-5-Sulphonate
Authors: Davies, T.G. / Tunnah, P. / Meijer, L. / Marko, D. / Eisenbrand, G. / Endicott, J.A. / Noble, M.E.
History
DepositionOct 16, 2000Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 11, 2001Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A3
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)128,3606
Polymers127,6764
Non-polymers6852
Water6,648369
1
A: CELL DIVISION PROTEIN KINASE 2
B: CYCLIN A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1803
Polymers63,8382
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
C: CELL DIVISION PROTEIN KINASE 2
D: CYCLIN A3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)64,1803
Polymers63,8382
Non-polymers3421
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)73.801, 133.804, 150.436
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.999932, -0.011239, 0.003138), (0.010826, -0.793178, 0.608894), (-0.004354, 0.608886, 0.793246)
Vector: 174.44279, -1.514, 0.7045)

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Components

#1: Protein CELL DIVISION PROTEIN KINASE 2 / CYCLIN-DEPENDENT KINASE 2 / CDK2


Mass: 33873.195 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: PHOSPHORYLATED ON THR 160 CHAINS A AND C ARE ASYMETRIC UNIT COPIES
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P24941, EC: 2.7.1.37
#2: Protein CYCLIN A3 / A3


Mass: 29964.713 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: TRUNCATED FRAGMENT OF CYCLIN A. IN COMPLEX WITH CDK2 CHAINS B AND D ARE ASYMETRIC UNIT COPIES
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P20248
#3: Chemical ChemComp-INR / 2',3-DIOXO-1,1',2',3-TETRAHYDRO-2,3'-BIINDOLE-5'-SULFONIC ACID / INDIRUBIN-5-SULPHONATE


Mass: 342.326 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C16H10N2O5S
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 369 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHE CDK2 SHOWS MAXIMAL ACTIVITY DURING S PHASE AND G2 AND INTERACTS WITH CYCLINS A, D, OR E. IT IS ...THE CDK2 SHOWS MAXIMAL ACTIVITY DURING S PHASE AND G2 AND INTERACTS WITH CYCLINS A, D, OR E. IT IS PROBABLY INVOLVED IN THE CONTROL OF THE CELL CYCLE. CYCLIN IS ESSENTIAL FOR THE CONTROL OF THE CELL CYCLE AT THE G1/S(START) AND THE G2/M (MITOSIS) TRANSITIONS.
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: 2.91 Å3/Da / Density % sol: 57.71 %
Crystal growpH: 7 / Details: pH 7.00
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
110 mg/mlprotein1drop
240 mMHEPES1drop
31 mMdithiothreitol1drop
4200 mM1dropNaCl
55 %(v/v)DMSO1drop
65 mMindirubin-5-sulphonate1drop
70.8 M1reservoirKCl
81.2 Mammonium sulfate1reservoir
940 mMHEPES1reservoir
105 mMdithiothreitol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 / Wavelength: 0.933
DetectorDate: Apr 15, 2000
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.933 Å / Relative weight: 1
ReflectionResolution: 2.5→20 Å / Num. obs: 47127 / % possible obs: 90.1 % / Redundancy: 3 % / Rmerge(I) obs: 0.109 / Net I/σ(I): 4.1
Reflection shellResolution: 2.5→2.59 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.39 / Mean I/σ(I) obs: 1.9 / % possible all: 90.1
Reflection
*PLUS
Highest resolution: 2.5 Å / Lowest resolution: 20 Å / Num. measured all: 143005 / Rmerge(I) obs: 0.103
Reflection shell
*PLUS
% possible obs: 63.8 % / Rmerge(I) obs: 0.388

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Processing

Software
NameVersionClassification
CNS1refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED STRUCTURE

Resolution: 2.5→100 Å / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.273 -5 %RANDOM
Rwork0.225 ---
obs0.225 52335 90 %-
Refinement stepCycle: LAST / Resolution: 2.5→100 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8938 0 48 369 9355
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.459
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it
Software
*PLUS
Name: CNS / Version: 1 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 100 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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