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Open data
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Basic information
Entry | Database: PDB / ID: 5iza | ||||||
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Title | Protein-protein interaction | ||||||
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![]() | PROTEIN BINDING/INHIBITOR / APC / ASEF / Colon CANCER / Drug discovery / PROTEIN BINDING-INHIBITOR complex | ||||||
Function / homology | ![]() APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity ...APC truncation mutants are not K63 polyubiquitinated / regulation of microtubule-based movement / negative regulation of cell cycle G1/S phase transition / gamma-catenin binding / regulation of attachment of spindle microtubules to kinetochore / positive regulation of pseudopodium assembly / positive regulation of protein localization to centrosome / pattern specification process / bicellular tight junction assembly / negative regulation of cyclin-dependent protein serine/threonine kinase activity / negative regulation of microtubule depolymerization / APC truncation mutants have impaired AXIN binding / AXIN missense mutants destabilize the destruction complex / Truncations of AMER1 destabilize the destruction complex / beta-catenin destruction complex / heart valve development / regulation of microtubule-based process / microtubule plus-end binding / protein kinase regulator activity / Beta-catenin phosphorylation cascade / Signaling by GSK3beta mutants / CTNNB1 S33 mutants aren't phosphorylated / CTNNB1 S37 mutants aren't phosphorylated / CTNNB1 S45 mutants aren't phosphorylated / CTNNB1 T41 mutants aren't phosphorylated / catenin complex / Wnt signalosome / Disassembly of the destruction complex and recruitment of AXIN to the membrane / cell fate specification / endocardial cushion morphogenesis / negative regulation of G1/S transition of mitotic cell cycle / dynein complex binding / mitotic spindle assembly checkpoint signaling / Apoptotic cleavage of cellular proteins / regulation of cell differentiation / cytoplasmic microtubule / mitotic cytokinesis / lateral plasma membrane / bicellular tight junction / Deactivation of the beta-catenin transactivating complex / adherens junction / Degradation of beta-catenin by the destruction complex / negative regulation of canonical Wnt signaling pathway / kinetochore / beta-catenin binding / Wnt signaling pathway / ruffle membrane / positive regulation of protein catabolic process / Ovarian tumor domain proteases / cell migration / insulin receptor signaling pathway / lamellipodium / nervous system development / positive regulation of cold-induced thermogenesis / microtubule binding / protein-containing complex assembly / proteasome-mediated ubiquitin-dependent protein catabolic process / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / ubiquitin protein ligase binding / DNA damage response / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Zhao, Y. / Jiang, H. / Yang, X. / Jiang, F. / Song, K. / Zhang, J. | ||||||
![]() | ![]() Title: Peptidomimetic inhibitors of APC-Asef interaction block colorectal cancer migration. Authors: Jiang, H. / Deng, R. / Yang, X. / Shang, J. / Lu, S. / Zhao, Y. / Song, K. / Liu, X. / Zhang, Q. / Chen, Y. / Chinn, Y.E. / Wu, G. / Li, J. / Chen, G. / Yu, J. / Zhang, J. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 174.5 KB | Display | ![]() |
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PDB format | ![]() | 137.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 435 KB | Display | ![]() |
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Full document | ![]() | 438 KB | Display | |
Data in XML | ![]() | 18.2 KB | Display | |
Data in CIF | ![]() | 28 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 5b6gC ![]() 5iz6C ![]() 5iz8C ![]() 5iz9C ![]() 3nmwS C: citing same article ( 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: 39268.246 Da / Num. of mol.: 1 / Fragment: UNP RESIDUES 407-751 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() |
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#2: Protein/peptide | Mass: 726.801 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) ![]() |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.8 Å3/Da / Density % sol: 31.7 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 8 Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 93 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 15, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→51.78 Å / Num. obs: 46357 / % possible obs: 99.5 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.545 / Rsym value: 0.064 / Net I/σ(I): 21.27 |
Reflection shell | Resolution: 1.5→1.55 Å / Redundancy: 4.7 % / Rmerge(I) obs: 0.545 / Mean I/σ(I) obs: 2.86 / % possible all: 99.9 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3NMW Resolution: 1.5→51.78 Å / Cor.coef. Fo:Fc: 0.982 / Cor.coef. Fo:Fc free: 0.973 / SU B: 2.84 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.089 / ESU R Free: 0.067 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 24.03 Å2
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Refinement step | Cycle: 1 / Resolution: 1.5→51.78 Å
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