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Open data
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Basic information
Entry | Database: PDB / ID: 6twu | ||||||
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Title | MAGI1_2 complexed with a phosphomimetic 16E6 peptide | ||||||
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![]() | PEPTIDE BINDING PROTEIN / phosphorylation / motif / PDZ domain | ||||||
Function / homology | ![]() positive regulation of low-density lipoprotein particle receptor binding / symbiont-mediated suppression of host transcription / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / positive regulation of vesicle fusion / negative regulation of low-density lipoprotein particle receptor catabolic process ...positive regulation of low-density lipoprotein particle receptor binding / symbiont-mediated suppression of host transcription / positive regulation of receptor-mediated endocytosis involved in cholesterol transport / AnxA2-p11 complex / membrane raft assembly / positive regulation of vacuole organization / positive regulation of low-density lipoprotein particle clearance / phospholipase A2 inhibitor activity / 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 / positive regulation of cell-cell adhesion / myelin sheath adaxonal region / cadherin binding involved in cell-cell adhesion / Schmidt-Lanterman incisure / vesicle budding from membrane / cornified envelope / plasma membrane protein complex / regulation of proteolysis / calcium-dependent phospholipid binding / negative regulation of receptor internalization / activation of GTPase activity / 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 / positive regulation of receptor recycling / phosphatidylserine binding / alpha-actinin binding / positive regulation of exocytosis / basement membrane / regulation of neurogenesis / Smooth Muscle Contraction / bicellular tight junction / 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 / cell projection / cell periphery / PDZ domain binding / adherens junction / lung development / calcium channel activity / mRNA transcription by RNA polymerase II / serine-type endopeptidase inhibitor activity / sarcolemma / nuclear matrix / RNA polymerase II transcription regulator complex / calcium-dependent protein binding / azurophil granule lumen / cell-cell junction / melanosome / cell junction / late endosome membrane / midbody / symbiont-mediated suppression of host cytoplasmic pattern recognition receptor signaling pathway via inhibition of IRF3 activity / protein-containing complex assembly / basolateral plasma membrane / symbiont-mediated perturbation of host ubiquitin-like protein modification / angiogenesis / collagen-containing extracellular matrix / protease binding / vesicle / host cell cytoplasm / cell surface receptor signaling pathway / early endosome / cell adhesion / endosome / symbiont-mediated suppression of host type I interferon-mediated signaling pathway / lysosomal membrane / virus-mediated perturbation of host defense response / DNA-templated transcription / calcium ion binding / host cell nucleus / Neutrophil degranulation / nucleolus / cell surface / signal transduction / positive regulation of transcription by RNA polymerase II / DNA binding / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / ATP binding / identical protein binding / membrane / nucleus / metal ion binding / plasma membrane Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Gogl, G. / Cousido-Siah, A. / Trave, G. | ||||||
![]() | ![]() Title: Dual Specificity PDZ- and 14-3-3-Binding Motifs: A Structural and Interactomics Study. Authors: Gogl, G. / Jane, P. / Caillet-Saguy, C. / Kostmann, C. / Bich, G. / Cousido-Siah, A. / Nyitray, L. / Vincentelli, R. / Wolff, N. / Nomine, Y. / Sluchanko, N.N. / Trave, 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 | ![]() | 396.5 KB | Display | ![]() |
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PDB format | ![]() | 291.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 475.4 KB | Display | ![]() |
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Full document | ![]() | 491.1 KB | Display | |
Data in XML | ![]() | 31.9 KB | Display | |
Data in CIF | ![]() | 43.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6twqC ![]() 6twxC ![]() 6twyC ![]() 6twzC ![]() 5n7dS S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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Unit cell |
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Components
-Protein / Protein/peptide , 2 types, 3 molecules ABC
#1: Protein | Mass: 48099.840 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() Gene: MAGI1, AIP3, BAIAP1, BAP1, TNRC19, ANXA2, ANX2, ANX2L4, CAL1H, LPC2D Production host: ![]() ![]() #2: Protein/peptide | | Mass: 1264.370 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
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-Non-polymers , 4 types, 79 molecules ![](data/chem/img/GOL.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
![](data/chem/img/CIT.gif)
![](data/chem/img/CA.gif)
![](data/chem/img/HOH.gif)
#3: Chemical | #4: Chemical | #5: Chemical | ChemComp-CA / #6: Water | ChemComp-HOH / | |
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-Details
Has ligand of interest | N |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.99 Å3/Da / Density % sol: 58.88 % |
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Crystal grow | Temperature: 296 K / Method: vapor diffusion, hanging drop Details: 22% PEG3000, 100mM Na-citrate (pH5.5), 100mM Na-citrate |
-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: Dec 9, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→48.3 Å / Num. obs: 46699 / % possible obs: 99.9 % / Redundancy: 13.2 % / Biso Wilson estimate: 65.37 Å2 / CC1/2: 1 / Net I/σ(I): 1.22 |
Reflection shell | Resolution: 2.4→2.46 Å / Mean I/σ(I) obs: 1.22 / Num. unique obs: 3389 / CC1/2: 0.489 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 5N7D Resolution: 2.4→48.22 Å / SU ML: 0.3968 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 29.4691
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 87.07 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→48.22 Å
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Refine LS restraints |
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LS refinement shell |
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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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