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- PDB-7pc7: The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding... -
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Basic information
Entry | Database: PDB / ID: 7pc7 | ||||||
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Title | The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of PTEN | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / complex / crystallization chaperone | ||||||
Function / homology | ![]() inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity ...inositol-1,3,4,5,6-pentakisphosphate 3-phosphatase activity / PTEN Loss of Function in Cancer / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase / regulation of cellular component size / negative regulation of keratinocyte migration / phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity / negative regulation of synaptic vesicle clustering / phosphatidylinositol phosphate phosphatase activity / rhythmic synaptic transmission / inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity / central nervous system myelin maintenance / negative regulation of wound healing, spreading of epidermal cells / phosphatidylinositol-3-phosphate phosphatase activity / syntrophin complex / central nervous system neuron axonogenesis / postsynaptic density assembly / neuron-neuron synaptic transmission / positive regulation of low-density lipoprotein particle receptor binding / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / dystrophin-associated glycoprotein complex / positive regulation of vacuole organization / negative regulation of dendritic spine morphogenesis / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / Regulation of PTEN mRNA translation / synapse maturation / presynaptic membrane assembly / Negative regulation of the PI3K/AKT network / cellular response to electrical stimulus / negative regulation of cell cycle G1/S phase transition / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process / positive regulation of plasma membrane repair / positive regulation of plasminogen activation / PCSK9-AnxA2 complex / negative regulation of axonogenesis / Transcriptional Regulation by MECP2 / myelin sheath adaxonal region / phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity / negative regulation of excitatory postsynaptic potential / negative regulation of organ growth / forebrain morphogenesis / cell communication / negative regulation of focal adhesion assembly / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / anaphase-promoting complex binding / vesicle budding from membrane / Hydrolases; Acting on ester bonds; Phosphoric-monoester hydrolases / phosphatidylinositol dephosphorylation / cornified envelope / dentate gyrus development / negative regulation of cyclin-dependent protein serine/threonine kinase activity / plasma membrane protein complex / positive regulation of ubiquitin protein ligase activity / spindle assembly involved in female meiosis / positive regulation of ubiquitin-dependent protein catabolic process / negative regulation of cell size / phosphatidylinositol biosynthetic process / calcium-dependent phospholipid binding / dendritic spine morphogenesis / negative regulation of receptor internalization / negative regulation of epithelial to mesenchymal transition / brain morphogenesis / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / virion binding / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / regulation of neuron projection development / myosin phosphatase activity / negative regulation of G1/S transition of mitotic cell cycle / protein serine/threonine phosphatase activity / molecular function inhibitor activity / positive regulation of receptor recycling / protein-serine/threonine phosphatase / ubiquitin-specific protease binding / phosphatidylserine binding / Synthesis of IP3 and IP4 in the cytosol / regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / negative regulation of peptidyl-serine phosphorylation / positive regulation of exocytosis / locomotor rhythm / negative regulation of vascular associated smooth muscle cell proliferation / negative regulation of cellular senescence / Synthesis of PIPs at the plasma membrane / positive regulation of excitatory postsynaptic potential / phosphoprotein phosphatase activity / social behavior / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / localization / negative regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / canonical Wnt signaling pathway / prepulse inhibition Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Cousido-Siah, A. / Trave, G. / Gogl, G. | ||||||
Funding support | 1items
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![]() | ![]() Title: A scalable strategy to solve structures of PDZ domains and their complexes. Authors: Cousido-Siah, A. / Carneiro, L. / Kostmann, C. / Ecsedi, P. / Nyitray, L. / Trave, G. / Gogl, G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 351.3 KB | Display | ![]() |
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PDB format | ![]() | 286.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.6 KB | Display | ![]() |
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Full document | ![]() | 491.4 KB | Display | |
Data in XML | ![]() | 34.8 KB | Display | |
Data in CIF | ![]() | 50.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pc3C ![]() 7pc4C ![]() 7pc5C ![]() 7pc8C ![]() 7pc9C ![]() 7pcbC ![]() 7qqlC ![]() 7qqmC ![]() 7qqnC ![]() 2pdzS ![]() 5n7dS S: Starting model for refinement C: citing same article ( |
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Similar structure data | Similarity search - Function & homology ![]() |
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Links
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Assembly
Deposited unit | ![]()
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2 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 46770.379 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #2: Protein/peptide | Mass: 1241.326 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: N-terminal biotin-ttds (trioxatridecan-succinamic acid) label Source: (synth.) ![]() References: UniProt: P60484, protein-serine/threonine phosphatase, protein-tyrosine-phosphatase, phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.86 Å3/Da / Density % sol: 57.06 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1 M Tris 8.5, 22 % v/v PEG Smear Broad |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Jun 14, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→46.687 Å / Num. obs: 63552 / % possible obs: 100 % / Redundancy: 13.36 % / CC1/2: 0.999 / Rrim(I) all: 0.14 / Net I/σ(I): 14.38 |
Reflection shell | Resolution: 2.1→2.15 Å / Mean I/σ(I) obs: 1.71 / Num. unique obs: 4649 / CC1/2: 0.57 / Rrim(I) all: 1.766 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N7D, 2PDZ Resolution: 2.1→46.687 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 20.95 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1.1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 188.45 Å2 / Biso mean: 56.4524 Å2 / Biso min: 19.41 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→46.687 Å
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0 / % reflection obs: 100 %
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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