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Yorodumi- PDB-3q1i: Polo-like kinase I Polo-box domain in complex with FMPPPMSpSM pho... -
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-Basic information
Entry | Database: PDB / ID: 3q1i | ||||||
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Title | Polo-like kinase I Polo-box domain in complex with FMPPPMSpSM phosphopeptide from TCERG1 | ||||||
Components |
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Keywords | TRANSFERASE / KINASE / PEPTIDE BINDING PROTEIN / 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 / transcription elongation factor 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 / ubiquitin-like protein conjugating enzyme binding / RNA polymerase binding / 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 / negative regulation of transcription elongation by RNA polymerase II / 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 / mRNA Splicing - Major Pathway / RNA splicing / Condensation of Prophase Chromosomes / mitotic spindle organization / regulation of cytokinesis / positive regulation of peptidyl-threonine phosphorylation / RHO GTPases Activate Formins / positive regulation of transcription elongation by RNA polymerase II / transcription coregulator activity / 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 / mRNA processing / kinetochore / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / G2/M transition of mitotic cell cycle / transcription corepressor activity / 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 / RNA polymerase II-specific DNA-binding transcription factor binding / transcription coactivator activity / regulation of cell cycle / protein kinase activity / protein ubiquitination / nuclear speck / protein phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.4 Å | ||||||
Authors | Sledz, P. / 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 | 3q1i.cif.gz | 100.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3q1i.ent.gz | 74.9 KB | Display | PDB format |
PDBx/mmJSON format | 3q1i.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3q1i_validation.pdf.gz | 464.2 KB | Display | wwPDB validaton report |
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Full document | 3q1i_full_validation.pdf.gz | 464.6 KB | Display | |
Data in XML | 3q1i_validation.xml.gz | 13 KB | Display | |
Data in CIF | 3q1i_validation.cif.gz | 18.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/q1/3q1i ftp://data.pdbj.org/pub/pdb/validation_reports/q1/3q1i | HTTPS FTP |
-Related structure data
Related structure data | 3p2wC 3p2zC 3p34C 3p35C 3p36C 3p37C 1umwS S: Starting model for refinement C: citing same article (ref.) |
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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
-Protein / Protein/peptide , 2 types, 2 molecules AE
#1: Protein | Mass: 26755.518 Da / Num. of mol.: 1 / Fragment: Polo-box domain, 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 | Mass: 1128.301 Da / Num. of mol.: 1 / Source method: obtained synthetically / Details: Synthetic phosphopeptide / References: UniProt: O14776 |
-Non-polymers , 4 types, 195 molecules
#3: Chemical | ChemComp-1PE / |
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#4: Chemical | ChemComp-PEG / |
#5: Chemical | ChemComp-PG0 / |
#6: 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: 1.85 Å3/Da / Density % sol: 33.64 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 Details: 30% PEG400, 0.1M MES, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9184 Å |
Detector | Date: Nov 17, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9184 Å / Relative weight: 1 |
Reflection | Resolution: 1.4→56.54 Å / Num. all: 40284 / Num. obs: 38959 / % possible obs: 97 % |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1UMW chain A Resolution: 1.4→56.54 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.949 / SU B: 1.994 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.075 / ESU R Free: 0.075 / 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: 17.809 Å2
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Refinement step | Cycle: LAST / Resolution: 1.4→56.54 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.4→1.436 Å / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 8.095 Å / Origin y: -0.323 Å / Origin z: 14.42 Å
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