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Yorodumi- PDB-6f3j: The crystal structure of Glycogen Phosphorylase in complex with 10a -
+Open data
-Basic information
Entry | Database: PDB / ID: 6f3j | ||||||
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Title | The crystal structure of Glycogen Phosphorylase in complex with 10a | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE | ||||||
Function / homology | Function and homology information 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 | Oryctolagus cuniculus (rabbit) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 2.2 Å | ||||||
Authors | Kyriakis, E. / Stamati, E.C.V. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D. | ||||||
Citation | Journal: Eur J Med Chem / Year: 2018 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6f3j.cif.gz | 337.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6f3j.ent.gz | 284.4 KB | Display | PDB format |
PDBx/mmJSON format | 6f3j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/f3/6f3j ftp://data.pdbj.org/pub/pdb/validation_reports/f3/6f3j | HTTPS FTP |
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-Related structure data
-Links
-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) Oryctolagus cuniculus (rabbit) / Tissue: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-IMP / |
#4: Chemical | ChemComp-CKQ / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.18 % |
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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: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.9795 Å |
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: 0.9795 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→128 Å / Num. obs: 49885 / % possible obs: 99.8 % / Redundancy: 10.6 % / Rmerge(I) obs: 0.229 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.2→2.27 Å / Redundancy: 9.7 % / Mean I/σ(I) obs: 5.5 / % possible all: 99.7 |
-Processing
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: native T-state of GPb Resolution: 2.2→90.89 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 7.445 / SU ML: 0.094 / Cross valid method: THROUGHOUT / ESU R: 0.182 / ESU R Free: 0.143 / 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 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.902 Å2
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Refinement step | Cycle: 1 / Resolution: 2.2→90.89 Å
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Refine LS restraints |
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