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- PDB-3ixe: Structural basis of competition between PINCH1 and PINCH2 for bin... -
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Basic information
Entry | Database: PDB / ID: 3ixe | ||||||
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Title | Structural basis of competition between PINCH1 and PINCH2 for binding to the ankyrin repeat domain of integrin-linked kinase | ||||||
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![]() | SIGNALING PROTEIN/SIGNALING PROTEIN / ILK / INTEGRIN-LINKED KINASE / PINCH / LIM / ANKYRIN REPEAT / ANK / IPP / INTEGRIN-MEDIATED SIGNALING / ANK REPEAT / LIM DOMAIN / ZINC / ATP-binding / Cell junction / Cell membrane / Kinase / Membrane / Nucleotide-binding / Phosphoprotein / Serine/threonine-protein kinase / Transferase / Alternative splicing / Metal-binding / Nucleus / SIGNALING PROTEIN-SIGNALING PROTEIN COMPLEX | ||||||
Function / homology | ![]() negative regulation of hepatocyte proliferation / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / positive regulation of integrin-mediated signaling pathway / nerve development / Cell-extracellular matrix interactions / fibroblast migration / myelination in peripheral nervous system / cell projection organization ...negative regulation of hepatocyte proliferation / Localization of the PINCH-ILK-PARVIN complex to focal adhesions / negative regulation of neural precursor cell proliferation / positive regulation of signal transduction / positive regulation of integrin-mediated signaling pathway / nerve development / Cell-extracellular matrix interactions / fibroblast migration / myelination in peripheral nervous system / cell projection organization / cell junction assembly / cell-cell junction organization / positive regulation of BMP signaling pathway / neural precursor cell proliferation / establishment or maintenance of epithelial cell apical/basal polarity / branching involved in ureteric bud morphogenesis / outflow tract morphogenesis / positive regulation of osteoblast differentiation / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of phosphorylation / tumor necrosis factor-mediated signaling pathway / sarcomere / phosphatidylinositol 3-kinase/protein kinase B signal transduction / substrate adhesion-dependent cell spreading / cell-matrix adhesion / integrin-mediated signaling pathway / cell morphogenesis / platelet aggregation / cell-cell adhesion / cell-cell junction / positive regulation of canonical Wnt signaling pathway / lamellipodium / positive regulation of canonical NF-kappaB signal transduction / non-specific serine/threonine protein kinase / positive regulation of protein phosphorylation / protein phosphorylation / focal adhesion / protein serine kinase activity / protein serine/threonine kinase activity / positive regulation of cell population proliferation / negative regulation of apoptotic process / protein kinase binding / positive regulation of DNA-templated transcription / ATP binding / membrane / nucleus / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chiswell, B.P. / Stiegler, A.L. / Boggon, T.J. / Calderwood, D.A. | ||||||
![]() | ![]() Title: Structural basis of competition between PINCH1 and PINCH2 for binding to the ankyrin repeat domain of integrin-linked kinase. Authors: Chiswell, B.P. / Stiegler, A.L. / Razinia, Z. / Nalibotski, E. / Boggon, T.J. / Calderwood, D.A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 72.3 KB | Display | ![]() |
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PDB format | ![]() | 52.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 431.5 KB | Display | ![]() |
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Full document | ![]() | 433 KB | Display | |
Data in XML | ![]() | 15 KB | Display | |
Data in CIF | ![]() | 22.6 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3f6qS S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 20256.865 Da / Num. of mol.: 1 / Fragment: Ankyrin repeat domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: Q13418, non-specific serine/threonine protein kinase | ||
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#2: Protein | Mass: 8477.479 Da / Num. of mol.: 1 / Fragment: LIM1 domain Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() | ||
#3: Chemical | #4: Water | ChemComp-HOH / | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.19 Å3/Da / Density % sol: 43.95 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion / pH: 6.5 Details: 8% PEG 550 MME, 0.1 M MES, pH 6.5, 0.2 uL 20% Benzamidine hydrochloride hydrate, VAPOR DIFFUSION, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 270 / Detector: CCD / Date: Apr 6, 2009 / Details: Toroidal focusing mirror |
Radiation | Monochromator: Si(111) channel cut monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→20 Å / Num. all: 20416 / Num. obs: 20416 / % possible obs: 100 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 7.2 % / Biso Wilson estimate: 12.403 Å2 / Rsym value: 0.136 / Net I/σ(I): 9.7 |
Reflection shell | Resolution: 1.9→1.97 Å / Redundancy: 7.3 % / Mean I/σ(I) obs: 3.3 / Num. unique all: 2002 / Rsym value: 0.414 / % possible all: 100 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3F6Q Resolution: 1.9→19.9 Å / Cor.coef. Fo:Fc: 0.948 / Cor.coef. Fo:Fc free: 0.887 / SU B: 3.254 / SU ML: 0.097 / Cross valid method: THROUGHOUT / ESU R: 0.161 / ESU R Free: 0.149 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: BABINET MODEL WITH MASK | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.198 Å2
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Refinement step | Cycle: LAST / Resolution: 1.9→19.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.901→1.95 Å / Total num. of bins used: 20
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