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- PDB-2fet: Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. ... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2fet | ||||||
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Title | Synthesis of C-D-Glycopyranosyl-Hydroquinones and-Benzoquinones. Inhibition of PTP1B. Inhibition of and binding to glycogen phosphorylase in the crystal | ||||||
![]() | Glycogen phosphorylase, muscle form | ||||||
![]() | TRANSFERASE / glycogenolysis / type 2 diabetes | ||||||
Function / homology | ![]() glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / skeletal muscle myofibril / pyridoxal phosphate binding / nucleotide binding Similarity search - Function | ||||||
Biological species | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chrysina, E.D. / Kosmopoulou, M.N. / Leonidas, D.D. / Oikonomakos, N.G. | ||||||
![]() | Journal: Eur.J.Org.Chem. / Year: 2007 Title: In the Search of Glycogen Phosphorylase Inhibitors: Synthesis of C-D-Glycopyranosylbenzo(hydro)quinones Inhibition of and Binding to Glycogen Phosphorylase in the Crystal Authors: He, L. / Zhang, Y.Z. / Tanoh, M. / Chen, G.-R. / Praly, J.-P. / Chrysina, E.D. / Tiraidis, C. / Kosmopoulou, M. / Leonidas, D.D. / Oikonomakos, N.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 | ![]() | 179.4 KB | Display | ![]() |
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PDB format | ![]() | 140.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 454.1 KB | Display | ![]() |
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Full document | ![]() | 464 KB | Display | |
Data in XML | ![]() | 17.1 KB | Display | |
Data in CIF | ![]() | 27.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2prjS 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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1 | ![]()
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2 |
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3 | ![]()
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Unit cell |
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Details | Dimeric glycogen phosphorylase is the physiologiacally active species |
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Components
#1: Protein | Mass: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: PYRIDOXAL-5'-PHOSPHATE bound / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-PLP / |
#3: Sugar | ChemComp-H53 / ( |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.45 Å3/Da / Density % sol: 49.87 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10 mM Bes buffer, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 31, 2003 |
Radiation | Monochromator: CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.803 Å / Relative weight: 1 |
Reflection | Resolution: 2.03→30 Å / Num. all: 56087 / Num. obs: 56087 / % possible obs: 91.7 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 31.7 Å2 / Rsym value: 0.056 / Net I/σ(I): 13.1 |
Reflection shell | Resolution: 2.03→2.09 Å / Redundancy: 3.6 % / Mean I/σ(I) obs: 3.6 / Num. unique all: 2654 / Rsym value: 0.486 / % possible all: 88.4 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 2PRJ Resolution: 2.03→30 Å / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 38.7 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.03→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.03→2.1 Å
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