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Yorodumi- PDB-4yee: beta2 carbohydrate binding module (CBM) of AMP-activated protein ... -
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Open data
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Basic information
| Entry | Database: PDB / ID: 4yee | ||||||||||||
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| Title | beta2 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclodextrin | ||||||||||||
Components | 5'-AMP-activated protein kinase subunit beta-2 | ||||||||||||
Keywords | SUGAR BINDING PROTEIN / carbohydrate binding module (CBM) / AMP-activated protein kinase (AMPK) / glycogen | ||||||||||||
| Function / homology | Function and homology informationAMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process ...AMPK inhibits chREBP transcriptional activation activity / Carnitine shuttle / Energy dependent regulation of mTOR by LKB1-AMPK / Regulation of TP53 Activity through Phosphorylation / Macroautophagy / TP53 Regulates Metabolic Genes / nucleotide-activated protein kinase complex / cAMP-dependent protein kinase complex / cellular response to nutrient levels / fatty acid biosynthetic process / positive regulation of cold-induced thermogenesis / apical plasma membrane / protein kinase binding / enzyme binding / signal transduction / nucleoplasm / nucleus / cytoplasm Similarity search - Function | ||||||||||||
| Biological species | ![]() | ||||||||||||
| Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | ||||||||||||
Authors | Mobbs, J. / Gorman, M.A. / Parker, M.W. / Gooley, P.R. / Griffin, M. | ||||||||||||
Citation | Journal: Biochem.J. / Year: 2015Title: Determinants of oligosaccharide specificity of the carbohydrate-binding modules of AMP-activated protein kinase. Authors: Mobbs, J.I. / Koay, A. / Di Paolo, A. / Bieri, M. / Petrie, E.J. / Gorman, M.A. / Doughty, L. / Parker, M.W. / Stapleton, D.I. / Griffin, M.D. / Gooley, P.R. | ||||||||||||
| History |
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Structure visualization
| Structure viewer | Molecule: Molmil Jmol/JSmol |
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Downloads & links
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Download
| PDBx/mmCIF format | 4yee.cif.gz | 669.7 KB | Display | PDBx/mmCIF format |
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| PDB format | pdb4yee.ent.gz | 569.5 KB | Display | PDB format |
| PDBx/mmJSON format | 4yee.json.gz | Tree view | PDBx/mmJSON format | |
| Others | Other downloads |
-Validation report
| Summary document | 4yee_validation.pdf.gz | 7.8 MB | Display | wwPDB validaton report |
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| Full document | 4yee_full_validation.pdf.gz | 7.9 MB | Display | |
| Data in XML | 4yee_validation.xml.gz | 83.2 KB | Display | |
| Data in CIF | 4yee_validation.cif.gz | 117.7 KB | Display | |
| Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ye/4yee ftp://data.pdbj.org/pub/pdb/validation_reports/ye/4yee | HTTPS FTP |
-Related structure data
| Related structure data | ![]() 4y0gC ![]() 4yefC ![]() 2f15S 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
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Components
| #1: Protein | Mass: 10022.198 Da / Num. of mol.: 18 / Fragment: UNP residues 74-155 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Polysaccharide | Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D- ...Cyclic alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-alpha-D-glucopyranose-(1-4)-[alpha-D-glucopyranose-(1-6)]alpha-D-glucopyranose #3: Chemical | ChemComp-GOL / #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
| Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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Sample preparation
| Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.47 % |
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| Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, sitting drop / pH: 7 Details: in 0.2 M lithium chloride, 20% w/v PEG 6000 and 0.1 M sodium HEPES pH 7 |
-Data collection
| Diffraction | Mean temperature: 100 K |
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| Diffraction source | Source: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å |
| Detector | Type: ADSC QUANTUM 210r / Detector: CCD / Date: Jun 20, 2013 |
| Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
| Radiation wavelength | Wavelength: 0.9537 Å / Relative weight: 1 |
| Reflection | Resolution: 2→48.38 Å / Num. obs: 127116 / % possible obs: 99.9 % / Redundancy: 7.6 % / Rmerge(I) obs: 0.084 / Rsym value: 0.098 / Net I/σ(I): 16.9 |
| Reflection shell | Resolution: 2→2.03 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.668 / Mean I/σ(I) obs: 2.8 / % possible all: 97.8 |
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Processing
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| Refinement | Method to determine structure: MOLECULAR REPLACEMENTStarting model: 2F15 Resolution: 2→43.38 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.932 / SU B: 7.721 / SU ML: 0.124 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.163 / 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: 32.5 Å2
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| Refinement step | Cycle: LAST / Resolution: 2→43.38 Å
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| Refine LS restraints |
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