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Yorodumi- PDB-3p36: Polo-like kinase I Polo-box domain in complex with DPPLHSpTA phos... -
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-Basic information
Entry | Database: PDB / ID: 3p36 | ||||||
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Title | Polo-like kinase I Polo-box domain in complex with DPPLHSpTA phosphopeptide from PBIP1 | ||||||
Components |
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Keywords | TRANSFERASE / phosphoprotein binding domain / Plk1 | ||||||
Function / homology | Function and homology information Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly ...Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / Golgi inheritance / synaptonemal complex disassembly / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / polo kinase / mitotic nuclear membrane disassembly / protein localization to nuclear envelope / Phosphorylation of Emi1 / metaphase/anaphase transition of mitotic cell cycle / synaptonemal complex / female meiosis chromosome segregation / regulation of protein binding / anaphase-promoting complex binding / Phosphorylation of the APC/C / outer kinetochore / negative regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of ubiquitin protein ligase activity / regulation of mitotic spindle assembly / microtubule bundle formation / Polo-like kinase mediated events / mitotic chromosome condensation / Golgi Cisternae Pericentriolar Stack Reorganization / sister chromatid cohesion / regulation of mitotic metaphase/anaphase transition / centrosome cycle / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / mitotic spindle assembly checkpoint signaling / double-strand break repair via alternative nonhomologous end joining / mitotic spindle pole / regulation of anaphase-promoting complex-dependent catabolic process / mitotic G2 DNA damage checkpoint signaling / mitotic sister chromatid segregation / establishment of mitotic spindle orientation / positive regulation of proteolysis / centriolar satellite / mitotic cytokinesis / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / Cyclin A/B1/B2 associated events during G2/M transition / Mitotic Prometaphase / EML4 and NUDC in mitotic spindle formation / Loss of Nlp from mitotic centrosomes / Loss of proteins required for interphase microtubule organization from the centrosome / Recruitment of mitotic centrosome proteins and complexes / protein localization to chromatin / Recruitment of NuMA to mitotic centrosomes / Resolution of Sister Chromatid Cohesion / Anchoring of the basal body to the plasma membrane / regulation of mitotic cell cycle / centriole / AURKA Activation by TPX2 / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / protein destabilization / APC/C:Cdh1 mediated degradation of Cdc20 and other APC/C:Cdh1 targeted proteins in late mitosis/early G1 / establishment of protein localization / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / The role of GTSE1 in G2/M progression after G2 checkpoint / microtubule cytoskeleton / Regulation of PLK1 Activity at G2/M Transition / double-strand break repair / positive regulation of proteasomal ubiquitin-dependent protein catabolic process / mitotic cell cycle / midbody / microtubule binding / peptidyl-serine phosphorylation / regulation of cell cycle / protein kinase activity / protein ubiquitination / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / chromatin / negative regulation of apoptotic process / protein kinase binding / negative regulation of transcription by RNA polymerase II / magnesium ion binding / nucleoplasm / ATP binding / identical protein binding / nucleus / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.59 Å | ||||||
Authors | Sledz, P. / Stubbs, C.J. / Hyvonen, M. / Abell, C. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2011 Title: From crystal packing to molecular recognition: prediction and discovery of a binding site on the surface of polo-like kinase 1 Authors: Sledz, P. / Stubbs, C.J. / Lang, S. / Yang, Y.Q. / McKenzie, G.J. / Venkitaraman, A.R. / Hyvonen, M. / Abell, C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3p36.cif.gz | 66.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3p36.ent.gz | 47.3 KB | Display | PDB format |
PDBx/mmJSON format | 3p36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3p36_validation.pdf.gz | 466.3 KB | Display | wwPDB validaton report |
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Full document | 3p36_full_validation.pdf.gz | 470.6 KB | Display | |
Data in XML | 3p36_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 3p36_validation.cif.gz | 19.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p3/3p36 ftp://data.pdbj.org/pub/pdb/validation_reports/p3/3p36 | HTTPS FTP |
-Related structure data
Related structure data | 3p2wC 3p2zC 3p34C 3p35C 3p37C 3q1iC 1umwS C: citing same article (ref.) S: Starting model for refinement |
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Similar 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: 26755.518 Da / Num. of mol.: 1 / Fragment: Polo-box domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pGEX-6p-1 / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase |
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#2: Protein/peptide | Mass: 941.922 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Chemically synthesized |
#3: Chemical | ChemComp-GOL / |
#4: Chemical | ChemComp-PO4 / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.95 Å3/Da / Density % sol: 36.83 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2 Details: 100mM Na/K phosphate, 0.2M NaCl, 10% PEG 8000, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 / Wavelength: 0.9334 Å |
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Detector | Date: Apr 22, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9334 Å / Relative weight: 1 |
Reflection | Resolution: 1.59→57.93 Å / Num. all: 27774 / Num. obs: 27603 / % possible obs: 99.4 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UMW (chain A) Resolution: 1.59→57.93 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.921 / SU B: 2.263 / SU ML: 0.08 / Cross valid method: THROUGHOUT / ESU R Free: 0.115 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.027 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.59→57.93 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.591→1.633 Å / Total num. of bins used: 20
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