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Yorodumi- PDB-4whh: A New Class of Peptidomimetics Targeting the Polo-box Domain of P... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4whh | |||||||||
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Title | A New Class of Peptidomimetics Targeting the Polo-box Domain of Polo-like kinase 1 | |||||||||
Components |
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Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Polo-like kinase / inhibitor / peptide derivative / 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) synthetic construct (others) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | |||||||||
Authors | Bang, J.K. | |||||||||
Funding support | Korea, Republic Of, 2items
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Citation | Journal: J.Med.Chem. / Year: 2015 Title: A new class of peptidomimetics targeting the polo-box domain of polo-like kinase 1. Authors: Ahn, M. / Han, Y.H. / Park, J.E. / Kim, S. / Lee, W.C. / Lee, S.J. / Gunasekaran, P. / Cheong, C. / Shin, S.Y. / Kim, H.Y. / Ryu, E.K. / Murugan, R.N. / Kim, N.H. / Bang, J.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4whh.cif.gz | 63.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4whh.ent.gz | 43.1 KB | Display | PDB format |
PDBx/mmJSON format | 4whh.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4whh_validation.pdf.gz | 456.3 KB | Display | wwPDB validaton report |
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Full document | 4whh_full_validation.pdf.gz | 459.1 KB | Display | |
Data in XML | 4whh_validation.xml.gz | 11.3 KB | Display | |
Data in CIF | 4whh_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/wh/4whh ftp://data.pdbj.org/pub/pdb/validation_reports/wh/4whh | HTTPS FTP |
-Related structure data
Related structure data | 4rcpC 4whkC 4whlC 3rq7S 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: 27285.158 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 371-603 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PLK1, PLK / Plasmid: pET28 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P53350, polo kinase | ||
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#2: Protein/peptide | | ||
#3: Chemical | #4: 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: 2.03 Å3/Da / Density % sol: 39.4 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 / Details: 0.1M HEPES, 2.0M Ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 93 K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: PAL/PLS / Beamline: 7A (6B, 6C1) / Wavelength: 0.97934 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 19, 2014 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.97934 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.9→50 Å / Num. obs: 18067 / % possible obs: 97.6 % / Redundancy: 11.5 % / Rmerge(I) obs: 0.069 / Χ2: 2.722 / Net I/av σ(I): 53.909 / Net I/σ(I): 15.1 / Num. measured all: 208591 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1 / Rejects: _
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3RQ7 Resolution: 1.9→43.91 Å / Cor.coef. Fo:Fc: 0.943 / Cor.coef. Fo:Fc free: 0.92 / WRfactor Rfree: 0.2358 / WRfactor Rwork: 0.1901 / FOM work R set: 0.8576 / SU B: 3.053 / SU ML: 0.091 / SU R Cruickshank DPI: 0.1591 / SU Rfree: 0.1495 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.159 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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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 max: 101.64 Å2 / Biso mean: 32.986 Å2 / Biso min: 15.93 Å2
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Refinement step | Cycle: final / Resolution: 1.9→43.91 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.895→1.944 Å / Total num. of bins used: 20
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