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Yorodumi- PDB-1fq1: CRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) IN COMPL... -
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-Basic information
Entry | Database: PDB / ID: 1fq1 | ||||||
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Title | CRYSTAL STRUCTURE OF KINASE ASSOCIATED PHOSPHATASE (KAP) IN COMPLEX WITH PHOSPHO-CDK2 | ||||||
Components |
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Keywords | Hydrolase/Transferase / phospho-protein-protein complex / Hydrolase-Transferase COMPLEX | ||||||
Function / homology | Function and homology information protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / 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 ...protein tyrosine/serine/threonine phosphatase activity / myosin phosphatase activity / protein serine/threonine phosphatase activity / protein-serine/threonine phosphatase / 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 cyclin-dependent protein serine/threonine kinase activity / 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 / cyclin-dependent protein kinase holoenzyme complex / cellular response to nitric oxide / Cajal body / 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 / dephosphorylation / Cyclin A:Cdk2-associated events at S phase entry / condensed chromosome / mitotic G1 DNA damage checkpoint signaling / regulation of G2/M transition of mitotic cell cycle / cyclin binding / post-translational protein modification / protein-tyrosine-phosphatase / meiotic cell cycle / male germ cell nucleus / response to organic substance / protein tyrosine phosphatase activity / G1/S transition of mitotic cell cycle / potassium ion transport / DNA Damage/Telomere Stress Induced Senescence / CDK-mediated phosphorylation and removal of Cdc6 / SCF(Skp2)-mediated degradation of p27/p21 / Meiotic recombination / Orc1 removal from chromatin / Transcriptional regulation of granulopoiesis / Cyclin D associated events in G1 / G2/M transition of mitotic cell cycle / 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 / Ras protein signal transduction / Regulation of TP53 Activity through Phosphorylation / transcription regulator complex / DNA replication / chromosome, telomeric region / regulation of cell cycle / endosome / chromatin remodeling / cell division / protein domain specific binding / negative regulation of cell population proliferation / protein phosphorylation / DNA repair / protein serine kinase activity / centrosome / protein serine/threonine kinase activity / DNA-templated transcription / positive regulation of cell population proliferation / perinuclear region of cytoplasm / positive regulation of DNA-templated transcription / negative regulation of transcription by RNA polymerase II / magnesium ion binding / signal transduction / nucleoplasm / ATP binding / nucleus / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3 Å | ||||||
Authors | Song, H. / Hanlon, N. / Brown, N.R. / Noble, M.E.M. / Johnson, L.N. / Barford, D. | ||||||
Citation | Journal: Mol.Cell / Year: 2001 Title: Phosphoprotein-protein interactions revealed by the crystal structure of kinase-associated phosphatase in complex with phosphoCDK2. Authors: Song, H. / Hanlon, N. / Brown, N.R. / Noble, M.E. / Johnson, L.N. / Barford, D. #1: Journal: Science / Year: 1995 Title: Dephosphorylation of Cdk2 Thr160 by the cyclin dependent kinase-interacting phosphatase KAP in the absence of cyclin Authors: Poon, R.Y.C. / Hunter, T. #2: Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: Cdi1, a human G1 and S phase protein phosphatase that associates with Cdk2 Authors: Gyruris, J. / Golemis, E. / Chertkov, H. / Brent, R. #3: Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: The p21Cdk-interacting protein Cip1 is a potent inhibitor of G1 cyclin-dependent kinases Authors: Harper, J.W. / Adami, G.R. / Wei, N. / Keyomarsi, K. / Elledge, S.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fq1.cif.gz | 105.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fq1.ent.gz | 85.4 KB | Display | PDB format |
PDBx/mmJSON format | 1fq1.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fq/1fq1 ftp://data.pdbj.org/pub/pdb/validation_reports/fq/1fq1 | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23819.057 Da / Num. of mol.: 1 / Mutation: C140S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: Q16667, protein-tyrosine-phosphatase |
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#2: Protein | Mass: 34056.469 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Description: HOMO SAPIENS / Production host: Escherichia coli (E. coli) / References: UniProt: P24941, cyclin-dependent kinase |
#3: Chemical | ChemComp-MG / |
#4: Chemical | ChemComp-ATP / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.96 Å3/Da / Density % sol: 58.52 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 6.5 Details: PEG 8000,KCl, Mgacetate,Na cacodylate , pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 4 ℃ | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: BM14 |
Detector | Type: ADSC / Detector: CCD / Date: Jan 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3→30 Å / Num. obs: 17091 / % possible obs: 99.7 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 5.3 % / Biso Wilson estimate: 95.5 Å2 / Rmerge(I) obs: 0.073 / Net I/σ(I): 5.6 |
Reflection shell | Resolution: 3→3.13 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.36 / % possible all: 99.9 |
Reflection | *PLUS Num. measured all: 89741 |
Reflection shell | *PLUS % possible obs: 99.6 % / Mean I/σ(I) obs: 1.8 |
-Processing
Software |
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Refinement | Resolution: 3→20 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 3→20 Å
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Refine LS restraints |
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Software | *PLUS Name: CNS / Classification: refinement | ||||||||||||||||||||
Refinement | *PLUS Highest resolution: 3 Å / Lowest resolution: 20 Å / σ(F): 0 / % reflection Rfree: 10 % / Rfactor obs: 0.235 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||
Refine LS restraints | *PLUS Type: c_angle_deg / Dev ideal: 1.8 |