[English] 日本語
Yorodumi- PDB-2v5q: CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WIT... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2v5q | ||||||
---|---|---|---|---|---|---|---|
Title | CRYSTAL STRUCTURE OF WILD-TYPE PLK-1 KINASE DOMAIN IN COMPLEX WITH A SELECTIVE DARPIN | ||||||
Components |
| ||||||
Keywords | TRANSFERASE / DESIGN ANKYRIN REPEAT PROTEIN / TRANSFERASE COMPLEX / PHOSPHORYLATION / NUCLEOTIDE-BINDING / SERINE/THREONINE-PROTEIN KINASE / KINASE / NUCLEUS / ATP-BINDING / SERINE/THREONINE PROTEIN KINASE | ||||||
Function / homology | Function and homology information regulation of anaphase-promoting complex-dependent catabolic process / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / regulation of protein binding ...regulation of anaphase-promoting complex-dependent catabolic process / Mitotic Telophase/Cytokinesis / regulation of protein localization to cell cortex / Mitotic Metaphase/Anaphase Transition / synaptonemal complex disassembly / Golgi inheritance / Activation of NIMA Kinases NEK9, NEK6, NEK7 / homologous chromosome segregation / nuclear membrane disassembly / regulation of protein binding / 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 / anaphase-promoting complex binding / outer kinetochore / Phosphorylation of the APC/C / 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 / Regulation of MITF-M-dependent genes involved in cell cycle and proliferation / sister chromatid cohesion / centrosome cycle / regulation of mitotic metaphase/anaphase transition / positive regulation of ubiquitin-protein transferase activity / regulation of mitotic cell cycle phase transition / double-strand break repair via alternative nonhomologous end joining / mitotic spindle assembly checkpoint signaling / Cyclin A/B1/B2 associated events during G2/M transition / mitotic spindle pole / regulation of mitotic cell cycle / establishment of mitotic spindle orientation / mitotic sister chromatid segregation / mitotic G2 DNA damage checkpoint signaling / positive regulation of proteolysis / mitotic cytokinesis / centriolar satellite / spindle midzone / negative regulation of double-strand break repair via homologous recombination / Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal / 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 / Anchoring of the basal body to the plasma membrane / Resolution of Sister Chromatid Cohesion / 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 / G2/M transition of mitotic cell cycle / spindle pole / positive regulation of protein localization to nucleus / spindle / Separation of Sister Chromatids / 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 / peptidyl-serine phosphorylation / midbody / microtubule binding / 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: 2.3 Å | ||||||
Authors | Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghaenel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Puetter, V. / Amstutz, P. ...Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghaenel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Puetter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / Holz, C. / Schmitz, A.A.P. / Lang, C. / Donner, P. / Egner, U. / Carrondo, M.A. / Mueller-Tiemann, B. | ||||||
Citation | Journal: Acta Crystallogr. D Biol. Crystallogr. / Year: 2008 Title: Structure of wild-type Plk-1 kinase domain in complex with a selective DARPin. Authors: Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghanel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Putter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / ...Authors: Bandeiras, T.M. / Hillig, R.C. / Matias, P.M. / Eberspaecher, U. / Fanghanel, J. / Thomaz, M. / Miranda, S. / Crusius, K. / Putter, V. / Amstutz, P. / Gulotti-Georgieva, M. / Binz, H.K. / Holz, C. / Schmitz, A.A. / Lang, C. / Donner, P. / Egner, U. / Carrondo, M.A. / Muller-Tiemann, B. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 2v5q.cif.gz | 180.8 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb2v5q.ent.gz | 142.7 KB | Display | PDB format |
PDBx/mmJSON format | 2v5q.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2v5q_validation.pdf.gz | 386.4 KB | Display | wwPDB validaton report |
---|---|---|---|---|
Full document | 2v5q_full_validation.pdf.gz | 394.2 KB | Display | |
Data in XML | 2v5q_validation.xml.gz | 16.5 KB | Display | |
Data in CIF | 2v5q_validation.cif.gz | 28.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/v5/2v5q ftp://data.pdbj.org/pub/pdb/validation_reports/v5/2v5q | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 35972.875 Da / Num. of mol.: 2 / Fragment: KINASE DOMAIN, RESIDUES 33-345 Source method: isolated from a genetically manipulated source Details: CONSTRUCT 4 / Source: (gene. exp.) HOMO SAPIENS (human) / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) / References: UniProt: P53350, polo kinase #2: Protein | Mass: 17835.967 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Details: VARIANT 3H10 / Source: (gene. exp.) synthetic construct (others) / Description: DESIGNED PROTEIN / Production host: ESCHERICHIA COLI (E. coli) #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.7 Å3/Da / Density % sol: 54 % |
---|---|
Crystal grow | Temperature: 303 K Details: 0.1 M TRIS-HCL PH 8.0, 8% PEG 5000 MME, 0.01 M EDTA SODIUM SALT AT 303 K. |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.037 |
Detector | Type: ADSC CCD / Detector: CCD / Date: Jul 20, 2006 / Details: MIRRORS |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.037 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→96.2 Å / Num. obs: 51702 / % possible obs: 99.3 % / Redundancy: 3.5 % / Biso Wilson estimate: 45.7 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 15.7 |
Reflection shell | Resolution: 2.3→2.42 Å / Redundancy: 3.6 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 3.3 / % possible all: 99.3 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PLK-1 - HOMOLOGY MODEL FROM PDB ENTRY 1OL5 DARPIN 3H10 - PDB ENTRY 1MJ0 TRUNCATED AFTER RESIDUE 141 Resolution: 2.3→61.08 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.928 / SU B: 11.227 / SU ML: 0.145 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.245 / ESU R Free: 0.198 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 34.28 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.3→61.08 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|