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- PDB-7qqn: The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding... -
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Open data
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Basic information
Entry | Database: PDB / ID: 7qqn | ||||||
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Title | The PDZ domain of SNTG1 complexed with the acetylated PDZ-binding motif of TRPV3 | ||||||
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![]() | PEPTIDE BINDING PROTEIN / PDZ / linear motif / crystallization chaperone | ||||||
Function / homology | ![]() syntrophin complex / 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 / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / negative regulation of hair cycle ...syntrophin complex / 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 / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / negative regulation of hair cycle / 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 / myelin sheath adaxonal region / cell communication / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / calcium-dependent phospholipid binding / negative regulation of receptor internalization / osmosensory signaling pathway / collagen fibril organization / Dissolution of Fibrin Clot / S100 protein binding / virion binding / TRP channels / positive regulation of low-density lipoprotein receptor activity / osteoclast development / epithelial cell apoptotic process / response to temperature stimulus / positive regulation of receptor recycling / positive regulation of calcium ion import / phosphatidylserine binding / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / calcium ion import across plasma membrane / Smooth Muscle Contraction / fibrinolysis / cytoskeletal protein binding / phosphatidylinositol-4,5-bisphosphate binding / Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation / lipid droplet / cell-matrix adhesion / response to activity / calcium ion transmembrane transport / actin filament organization / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / cilium / nuclear matrix / ruffle membrane / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / melanosome / late endosome membrane / actin binding / midbody / basolateral plasma membrane / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / early endosome / cytoskeleton / receptor complex / endosome / lysosomal membrane / calcium ion binding / Neutrophil degranulation / structural molecule activity / cell surface / positive regulation of transcription by RNA polymerase II / RNA binding / extracellular space / extracellular exosome / extracellular region / identical protein binding / membrane / nucleus / plasma membrane / cytoplasm / cytosol 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 | ![]() | 347.4 KB | Display | ![]() |
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PDB format | ![]() | 285.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 459.8 KB | Display | ![]() |
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Full document | ![]() | 466.3 KB | Display | |
Data in XML | ![]() | 31.3 KB | Display | |
Data in CIF | ![]() | 44.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 7pc3C ![]() 7pc4C ![]() 7pc5C ![]() 7pc7C ![]() 7pc8C ![]() 7pc9C ![]() 7pcbC ![]() 7qqlC ![]() 7qqmC ![]() 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: 1165.202 Da / Num. of mol.: 2 / Source method: obtained synthetically Details: N-terminal biotin-ado-ado linker (amino-dodecanoic acid) Source: (synth.) ![]() #3: Chemical | ChemComp-CA / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | N | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.62 Å3/Da / Density % sol: 52.99 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop Details: 0.15 M Lithium sulfate 0.05 M Magnesium chloride hexahydrate 0.1 M HEPES 7.8 20 % v/v PEG Smear High |
-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: Oct 25, 2021 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→45.467 Å / Num. obs: 35752 / % possible obs: 99.8 % / Redundancy: 6.66 % / CC1/2: 0.996 / Rrim(I) all: 0.222 / Net I/σ(I): 8.22 |
Reflection shell | Resolution: 2.45→2.51 Å / Redundancy: 6.66 % / Mean I/σ(I) obs: 1.18 / Num. unique obs: 2621 / CC1/2: 0.529 / Rrim(I) all: 2.042 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N7D Resolution: 2.45→45.467 Å / SU ML: 0.38 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 32.11 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 1 Å / VDW probe radii: 1.2 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 172.44 Å2 / Biso mean: 63.1659 Å2 / Biso min: 22.5 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.45→45.467 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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