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Yorodumi- PDB-6alz: Crystal structure of Protein Phosphatase 1 bound to the natural i... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6alz | ||||||||||||
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Title | Crystal structure of Protein Phosphatase 1 bound to the natural inhibitor Tautomycetin | ||||||||||||
Components | Serine/threonine-protein phosphatase PP1-alpha catalytic subunit | ||||||||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / Inhibitor / complex / HYDROLASE / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity ...regulation of glycogen catabolic process / PTW/PP1 phosphatase complex / glycogen granule / regulation of glycogen biosynthetic process / protein phosphatase 1 binding / cadherin binding involved in cell-cell adhesion / positive regulation of extrinsic apoptotic signaling pathway in absence of ligand / regulation of canonical Wnt signaling pathway / regulation of translational initiation / myosin phosphatase activity / glycogen metabolic process / protein serine/threonine phosphatase activity / branching morphogenesis of an epithelial tube / protein-serine/threonine phosphatase / dephosphorylation / Triglyceride catabolism / entrainment of circadian clock by photoperiod / Maturation of hRSV A proteins / phosphatase activity / telomere maintenance in response to DNA damage / phosphoprotein phosphatase activity / DARPP-32 events / ribonucleoprotein complex binding / protein dephosphorylation / Downregulation of TGF-beta receptor signaling / adherens junction / response to lead ion / lung development / circadian regulation of gene expression / regulation of circadian rhythm / Circadian Clock / presynapse / perikaryon / dendritic spine / cell division / glutamatergic synapse / nucleolus / extracellular exosome / nucleoplasm / nucleus / metal ion binding / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||||||||
Biological species | Homo sapiens (human) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.208 Å | ||||||||||||
Authors | Choy, M.S. / Peti, W. / Page, R. | ||||||||||||
Funding support | United States, 3items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2017 Title: PP1:Tautomycetin Complex Reveals a Path toward the Development of PP1-Specific Inhibitors. Authors: Choy, M.S. / Swingle, M. / D'Arcy, B. / Abney, K. / Rusin, S.F. / Kettenbach, A.N. / Page, R. / Honkanen, R.E. / Peti, W. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6alz.cif.gz | 141.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6alz.ent.gz | 108.6 KB | Display | PDB format |
PDBx/mmJSON format | 6alz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6alz_validation.pdf.gz | 894.2 KB | Display | wwPDB validaton report |
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Full document | 6alz_full_validation.pdf.gz | 901.4 KB | Display | |
Data in XML | 6alz_validation.xml.gz | 26.8 KB | Display | |
Data in CIF | 6alz_validation.cif.gz | 37.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/al/6alz ftp://data.pdbj.org/pub/pdb/validation_reports/al/6alz | HTTPS FTP |
-Related structure data
Related structure data | 4movS 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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2 |
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3 |
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Unit cell |
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Details | Monomer as determined by gel filtration |
-Components
-Protein , 1 types, 2 molecules AB
#1: Protein | Mass: 34162.148 Da / Num. of mol.: 2 / Fragment: residues 7-300 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PPP1CA, PPP1A / Production host: Escherichia coli (E. coli) References: UniProt: P62136, protein-serine/threonine phosphatase |
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-Non-polymers , 5 types, 299 molecules
#2: Chemical | ChemComp-MN / #3: Chemical | #4: Chemical | ChemComp-DMS / | #5: Chemical | ChemComp-CL / #6: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.56 Å3/Da / Density % sol: 51.89 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 20% PEG 6000, 1 M lithium chloride, 0.1 M Tris pH 8.0 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.98 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Feb 4, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.98 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→38.8222 Å / Num. obs: 35351 / % possible obs: 97.5 % / Redundancy: 7 % / Biso Wilson estimate: 36.82 Å2 / CC1/2: 0.996 / Rmerge(I) obs: 0.118 / Rpim(I) all: 0.047 / Rrim(I) all: 0.127 / Net I/σ(I): 8.9 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.814 / Num. unique obs: 2260 / CC1/2: 0.503 / Rpim(I) all: 0.427 / Rrim(I) all: 0.927 / % possible all: 72.9 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4MOV Resolution: 2.208→38.816 Å / SU ML: 0.24 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 21.61 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.208→38.816 Å
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Refine LS restraints |
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LS refinement shell |
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