+Open data
-Basic information
Entry | Database: PDB / ID: 8gsj | ||||||
---|---|---|---|---|---|---|---|
Title | APC-Asef tripeptide inhibitor | ||||||
Components | Adenomatous polyposis coli proteinFamilial adenomatous polyposis | ||||||
Keywords | PROTEIN BINDING/INHIBITOR / PROTEIN BINDING-INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information 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 / microtubule plus-end binding / heart valve development / regulation of microtubule-based process / 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 / 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 / proteasome-mediated ubiquitin-dependent protein catabolic process / protein-containing complex assembly / microtubule / cell adhesion / positive regulation of cell migration / positive regulation of apoptotic process / negative regulation of cell population proliferation / centrosome / DNA damage response / ubiquitin protein ligase binding / protein kinase binding / perinuclear region of cytoplasm / Golgi apparatus / nucleoplasm / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Zhang, J. / Wang, X.F. / Song, K. | ||||||
Funding support | China, 1items
| ||||||
Citation | Journal: To Be Published Title: APC-Asef tripeptide inhibitor Authors: Zhang, J. / Wang, X.F. / Song, K. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 8gsj.cif.gz | 83.5 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb8gsj.ent.gz | 60.5 KB | Display | PDB format |
PDBx/mmJSON format | 8gsj.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/gs/8gsj ftp://data.pdbj.org/pub/pdb/validation_reports/gs/8gsj | HTTPS FTP |
---|
-Related structure data
Related structure data | 5izaS S: Starting model for refinement |
---|---|
Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-Components
-Protein , 1 types, 1 molecules A
#1: Protein | Mass: 37408.191 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: APC / Cell line (production host): HEK293 / Production host: Homo sapiens (human) / References: UniProt: P25054 |
---|
-Non-polymers , 8 types, 100 molecules
#2: Chemical | ChemComp-K8C / | ||||
---|---|---|---|---|---|
#3: Chemical | ChemComp-GLU / | ||||
#4: Chemical | ChemComp-NAL / | ||||
#5: Chemical | ChemComp-LEU / | ||||
#6: Chemical | ChemComp-GJZ / ( | ||||
#7: Chemical | ChemComp-GOL / #8: Chemical | #9: Water | ChemComp-HOH / | |
-Details
Has ligand of interest | Y |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.26 Å3/Da / Density % sol: 45.54 % |
---|---|
Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop Details: 0.2M Ammonium sulfate, 0.1M Tris pH 8.0, 25% w/v PEG 4000 |
-Data collection
Diffraction | Mean temperature: 93 K / Serial crystal experiment: N |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.978 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jan 2, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.978 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→52.22 Å / Num. obs: 20548 / % possible obs: 99.9 % / Redundancy: 12.9 % / CC1/2: 1 / Net I/σ(I): 21.9 |
Reflection shell | Resolution: 2.1→2.16 Å / Num. unique obs: 1652 / CC1/2: 0.852 |
-Phasing
Phasing | Method: molecular replacement |
---|
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5IZA Resolution: 2.1→52.22 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.94 / SU B: 8.058 / SU ML: 0.196 / Cross valid method: FREE R-VALUE / σ(F): 0 / ESU R: 0.245 / ESU R Free: 0.207 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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 max: 134.55 Å2 / Biso mean: 60.471 Å2 / Biso min: 37.84 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 2.1→52.22 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.1→2.15 Å / Rfactor Rfree error: 0
|