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Yorodumi- PDB-4e67: The structure of the polo-box domain (PBD) of polo-like kinase 1 ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4.0E+67 | ||||||
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Title | The structure of the polo-box domain (PBD) of polo-like kinase 1 (Plk1) in complex with hydrocinnamoyl-derivatized PLHSpTA peptide | ||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Serine/threonine-protein kinase / TRANSFERASE / Phosphoprotein-binding domain / TRANSFERASE-TRANSFERASE INHIBITOR complex | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.1 Å | ||||||
Authors | Sledz, P. / Hyvonen, M. / Tan, Y.S. / Lang, S. / Spring, D. / Abell, C. / Best, R.B. | ||||||
Citation | Journal: Angew.Chem.Int.Ed.Engl. / Year: 2012 Title: Using ligand-mapping simulations to design a ligand selectively targeting a cryptic surface pocket of polo-like kinase 1. Authors: Tan, Y.S. / Sledz, P. / Lang, S. / Stubbs, C.J. / Spring, D.R. / Abell, C. / Best, R.B. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4e67.cif.gz | 60.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4e67.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 4e67.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4e67_validation.pdf.gz | 434.4 KB | Display | wwPDB validaton report |
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Full document | 4e67_full_validation.pdf.gz | 435.5 KB | Display | |
Data in XML | 4e67_validation.xml.gz | 10.8 KB | Display | |
Data in CIF | 4e67_validation.cif.gz | 14.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e6/4e67 ftp://data.pdbj.org/pub/pdb/validation_reports/e6/4e67 | HTTPS FTP |
-Related structure data
Related structure data | 3p2zS 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 (PBD), residues 371-594 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Production host: Escherichia coli (E. coli) / References: UniProt: P53350, polo kinase |
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#2: Protein/peptide | |
#3: 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: 1.86 Å3/Da / Density % sol: 33.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: 0.1 M HEPES (pH 7.5), 0.1 M sodium azide and 22% PEG 4000, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5406 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 15, 2011 |
Radiation | Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5406 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→56.84 Å / Num. all: 11989 / Num. obs: 11821 / % possible obs: 98.6 % / Observed criterion σ(I): 2 |
Reflection shell | Resolution: 2.1→2.2 Å / % possible all: 90.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3p2z Resolution: 2.1→56.84 Å / Cor.coef. Fo:Fc: 0.926 / Cor.coef. Fo:Fc free: 0.885 / SU B: 5.669 / SU ML: 0.156 / Cross valid method: THROUGHOUT / ESU R: 0.322 / ESU R Free: 0.231 / 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: 20.274 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.1→56.84 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Total num. of bins used: 20
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