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- PDB-6f3s: The crystal structure of Glycogen Phosphorylase in complex with 10d -
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Open data
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Basic information
Entry | Database: PDB / ID: 6f3s | ||||||
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Title | The crystal structure of Glycogen Phosphorylase in complex with 10d | ||||||
![]() | Glycogen phosphorylase, muscle form![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() | ||||||
![]() | Kyriakis, E. / Stamati, E.C.V. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D. | ||||||
![]() | ![]() Title: A multidisciplinary study of 3-( beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics ...Title: A multidisciplinary study of 3-( beta-d-glucopyranosyl)-5-substituted-1,2,4-triazole derivatives as glycogen phosphorylase inhibitors: Computation, synthesis, crystallography and kinetics reveal new potent inhibitors. Authors: Kun, S. / Begum, J. / Kyriakis, E. / Stamati, E.C.V. / Barkas, T.A. / Szennyes, E. / Bokor, E. / Szabo, K.E. / Stravodimos, G.A. / Sipos, A. / Docsa, T. / Gergely, P. / Moffatt, C. / ...Authors: Kun, S. / Begum, J. / Kyriakis, E. / Stamati, E.C.V. / Barkas, T.A. / Szennyes, E. / Bokor, E. / Szabo, K.E. / Stravodimos, G.A. / Sipos, A. / Docsa, T. / Gergely, P. / Moffatt, C. / Patraskaki, M.S. / Kokolaki, M.C. / Gkerdi, A. / Skamnaki, V.T. / Leonidas, D.D. / Somsak, L. / Hayes, J.M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 336.9 KB | Display | ![]() |
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PDB format | ![]() | 283.5 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | ![]() Mass: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PLP / ![]() |
#3: Chemical | ChemComp-CKW / ( |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.32 % |
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Crystal grow![]() | Temperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10 mM BES buffer |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Oct 13, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 1.9→116 Å / Num. obs: 77397 / % possible obs: 100 % / Redundancy: 14.8 % / Rmerge(I) obs: 0.143 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.9→1.94 Å / Redundancy: 15.1 % / Mean I/σ(I) obs: 3.1 / % possible all: 100 |
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Processing
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Refinement | Resolution: 1.9→116 Å / Cor.coef. Fo:Fc: 0.981 / Cor.coef. Fo:Fc free: 0.977 / SU B: 4.658 / SU ML: 0.066 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.092 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.7 Å / Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 41.959 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→116 Å
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Refine LS restraints |
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