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- PDB-2wfy: Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin... -
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Basic information
Entry | Database: PDB / ID: 2wfy | |||||||||
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Title | Truncation and Optimisation of Peptide Inhibitors of CDK2, Cyclin A Through Structure Guided Design | |||||||||
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![]() | TRANSFERASE / CDK2 / KINASE / CYCLIN / ACTIVE / NUCLEUS / MITOSIS / SERINE/THREONINE-PROTEIN KINASE / CYTOPLASM / INHIBITION / CELL CYCLE / ATP-BINDING / CELL DIVISION / PHOSPHOPROTEIN / NUCLEOTIDE-BINDING / POLYMORPHISM / BETA-PEPTIDE / CYCLIN GROOVE | |||||||||
Function / homology | ![]() Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / 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 ...Phosphorylation of proteins involved in the G2/M transition by Cyclin A:Cdc2 complexes / cyclin A2-CDK1 complex / cell cycle G1/S phase transition / cellular response to luteinizing hormone stimulus / mitotic cell cycle phase transition / 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 / cellular response to insulin-like growth factor stimulus / positive regulation of DNA biosynthetic process / cochlea development / cyclin A1-CDK2 complex / cyclin E2-CDK2 complex / cyclin E1-CDK2 complex / cellular response to platelet-derived growth factor stimulus / 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 DNA replication / 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 / animal organ regeneration / 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 / cellular response to estradiol stimulus / Cdc20:Phospho-APC/C mediated degradation of Cyclin A / 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 / positive regulation of fibroblast proliferation / Regulation of TP53 Degradation / nuclear envelope / Factors involved in megakaryocyte development and platelet production / Processing of DNA double-strand break ends / cellular response to hypoxia / 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 / Ub-specific processing proteases / 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 / protein kinase binding / positive regulation of DNA-templated transcription Similarity search - Function | |||||||||
Biological species | ![]() SYNTHETIC CONSTRUCT (others) | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Kontopidis, G. / Andrews, M.J. / McInnes, C. / Plater, A. / Innes, L. / Renachowski, S. / Cowan, A. / Fischer, P.M. | |||||||||
![]() | ![]() Title: Truncation and Optimisation of Peptide Inhibitors of Cyclin-Dependent Kinase 2-Cyclin a Through Structure-Guided Design. Authors: Kontopidis, G. / Andrews, M.J. / Mcinnes, C. / Plater, A. / Innes, L. / Renachowski, S. / Cowan, A. / Fischer, P.M. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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PDBx/mmCIF format | ![]() | 245.4 KB | Display | ![]() |
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PDB format | ![]() | 199.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.5 KB | Display | ![]() |
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Full document | ![]() | 505.6 KB | Display | |
Data in XML | ![]() | 47.8 KB | Display | |
Data in CIF | ![]() | 68.4 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2wevC ![]() 2whbC ![]() 1okvS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments: Component-ID: 1 / End auth comp-ID: LEU / End label comp-ID: LEU
NCS ensembles :
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Components
#1: Protein | Mass: 33976.488 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein | Mass: 29867.512 Da / Num. of mol.: 2 / Fragment: RESIDUES 173-432 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Protein/peptide | Mass: 630.807 Da / Num. of mol.: 2 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) #4: Water | ChemComp-HOH / | Nonpolymer details | CHAINS E AND F COULD BE REPRESENTED AS A SINGLE HETEROGEN WITH NAME: (S)-3-((S)-2-((S)-2-ACETAMIDO- ...CHAINS E AND F COULD BE REPRESENTE | Sequence details | FRACTION 172-432 CRYSTALLIS | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.02 % / Description: NONE |
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Crystal grow | pH: 7.8 / Details: PEG3350 30% V/V, 0.1M TRI-SODIUM CITRATE, pH 7.8 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC CCD / Detector: CCD / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.977 Å / Relative weight: 1 |
Reflection | Resolution: 2.53→40 Å / Num. obs: 46387 / % possible obs: 80 % / Observed criterion σ(I): 1.3 / Redundancy: 13 % / Rmerge(I) obs: 0.3 / Net I/σ(I): 9 |
Reflection shell | Resolution: 2.53→2.56 Å / Rmerge(I) obs: 0.3 / Mean I/σ(I) obs: 1.34 / % possible all: 70 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1OKV Resolution: 2.53→40 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.914 / SU B: 11.747 / SU ML: 0.252 / Cross valid method: THROUGHOUT / ESU R: 0.785 / ESU R Free: 0.323 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. RESIDUES 36-40 IN CHAIN A AND C ARE DISORDERED RESIDUES 323-325 IN CHAIN B NAD D ARE DISORDERED
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 52.652 Å2
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Refinement step | Cycle: LAST / Resolution: 2.53→40 Å
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Refine LS restraints |
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