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Yorodumi- PDB-2h9v: Structural basis for induced-fit binding of Rho-kinase to the inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h9v | ||||||
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Title | Structural basis for induced-fit binding of Rho-kinase to the inhibitor Y27632 | ||||||
Components | Rho-associated protein kinase 2 | ||||||
Keywords | TRANSFERASE / protein kinase-inhibitor complex | ||||||
Function / homology | Function and homology information positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization ...positive regulation of centrosome duplication / Rho-dependent protein serine/threonine kinase activity / regulation of cell junction assembly / embryonic morphogenesis / actomyosin structure organization / cortical actin cytoskeleton organization / mitotic cytokinesis / Rho protein signal transduction / smooth muscle contraction / regulation of actin cytoskeleton organization / regulation of circadian rhythm / small GTPase binding / rhythmic process / actin cytoskeleton organization / cytoskeleton / non-specific serine/threonine protein kinase / protein kinase activity / phosphorylation / protein serine kinase activity / protein serine/threonine kinase activity / centrosome / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Bos taurus (cattle) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 3.1 Å | ||||||
Authors | Yamaguchi, H. / Miwa, Y. / Kasa, M. / Kitano, K. / Amano, M. / Kaibuchi, K. / Hakoshima, T. | ||||||
Citation | Journal: J.Biochem.(Tokyo) / Year: 2006 Title: Structural basis for induced-fit binding of Rho-kinase to the inhibitor Y-27632 Authors: Yamaguchi, H. / Miwa, Y. / Kasa, M. / Kitano, K. / Amano, M. / Kaibuchi, K. / Hakoshima, T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h9v.cif.gz | 90.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h9v.ent.gz | 67.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h9/2h9v ftp://data.pdbj.org/pub/pdb/validation_reports/h9/2h9v | HTTPS FTP |
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-Related structure data
Related structure data | |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 45776.020 Da / Num. of mol.: 1 / Fragment: PROTEIN KINASE DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Bos taurus (cattle) / Plasmid: pFastBac-HTa / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: Q28021, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-Y27 / ( |
#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: 4.5 Å3/Da / Density % sol: 72.8 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8 Details: Sodium Citrate, FOS-Choline-9, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 90 K | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SPring-8 / Beamline: BL44XU / Wavelength: 0.9 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: Bruker DIP-6040 / Detector: CCD / Date: Dec 8, 2004 Details: a double-crystal monochromator and a horizontal focusing mirror | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Monochromator: a double-crystal monochromator and a horizontal focusing mirror Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 0.9 Å / Relative weight: 1 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 3.1→30 Å / Num. obs: 16013 / % possible obs: 99.5 % / Redundancy: 14.9 % / Rmerge(I) obs: 0.074 / Χ2: 1.211 / Net I/σ(I): 29.988 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Rfactor: 0.46 / Cor.coef. Fo:Fc: 0.501
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 3.1→30 Å / Cor.coef. Fo:Fc: 0.924 / Cor.coef. Fo:Fc free: 0.901 / SU B: 16.749 / SU ML: 0.292 / SU R Cruickshank DPI: 0.784 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.397
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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: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 60.967 Å2
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Refinement step | Cycle: LAST / Resolution: 3.1→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.1→3.18 Å / Total num. of bins used: 20
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