[English] 日本語
![](img/lk-miru.gif)
- PDB-4yee: beta2 carbohydrate binding module (CBM) of AMP-activated protein ... -
+
Open data
-
Basic information
Entry | Database: PDB / ID: 4yee | ||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Title | beta2 carbohydrate binding module (CBM) of AMP-activated protein kinase (AMPK) in complex with glucosyl-beta-cyclodextrin | ||||||||||||
![]() | 5'-AMP-activated protein kinase subunit beta-2 | ||||||||||||
![]() | SUGAR BINDING PROTEIN / carbohydrate binding module (CBM) / AMP-activated protein kinase (AMPK) / glycogen | ||||||||||||
Function / homology | ![]() AMPK inhibits chREBP transcriptional activation activity / Carnitine metabolism / 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 metabolism / 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 | ![]() ![]() ![]() | ||||||||||||
![]() | Mobbs, J. / Gorman, M.A. / Parker, M.W. / Gooley, P.R. / Griffin, M. | ||||||||||||
![]() | ![]() Title: 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 |
|
-
Structure visualization
Structure viewer | Molecule: ![]() ![]() |
---|
-
Downloads & links
-
Download
PDBx/mmCIF format | ![]() | 669.7 KB | Display | ![]() |
---|---|---|---|---|
PDB format | ![]() | 569.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 7.8 MB | Display | ![]() |
---|---|---|---|---|
Full document | ![]() | 7.9 MB | Display | |
Data in XML | ![]() | 83.2 KB | Display | |
Data in CIF | ![]() | 117.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 4y0gC ![]() 4yefC ![]() 2f15S C: citing same article ( S: Starting model for refinement |
---|---|
Similar structure data |
-
Links
-
Assembly
-
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 / | |
---|
-Experimental details
-Experiment
Experiment | Method: ![]() |
---|
-
Sample preparation
Crystal | Density Matthews: 2.64 Å3/Da / Density % sol: 53.47 % |
---|---|
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 |
---|---|
Diffraction source | Source: ![]() ![]() ![]() |
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 |
-
Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: ![]() Starting 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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→43.38 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
|