+Open data
-Basic information
Entry | Database: PDB / ID: 5owy | ||||||
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Title | Glycogen Phosphorylase in complex with KS252 | ||||||
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: 1.9 Å | ||||||
Authors | Kyriakis, E. / Stravodimos, G. / Kantsadi, A. / Chatzileontiadou, D. / Leonidas, D. | ||||||
Citation | Journal: Bioorg. Chem. / Year: 2018 Title: Probing the beta-pocket of the active site of human liver glycogen phosphorylase with 3-(C-beta-d-glucopyranosyl)-5-(4-substituted-phenyl)-1, 2, 4-triazole inhibitors. Authors: Kyriakis, E. / Solovou, T.G.A. / Kun, S. / Czifrak, K. / Szocs, B. / Juhasz, L. / Bokor, E. / Stravodimos, G.A. / Kantsadi, A.L. / Chatzileontiadou, D.S.M. / Skamnaki, V.T. / Somsak, L. / Leonidas, D.D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5owy.cif.gz | 338.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5owy.ent.gz | 285 KB | Display | PDB format |
PDBx/mmJSON format | 5owy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5owy_validation.pdf.gz | 1017.7 KB | Display | wwPDB validaton report |
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Full document | 5owy_full_validation.pdf.gz | 1019.6 KB | Display | |
Data in XML | 5owy_validation.xml.gz | 30.6 KB | Display | |
Data in CIF | 5owy_validation.cif.gz | 45.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ow/5owy ftp://data.pdbj.org/pub/pdb/validation_reports/ow/5owy | HTTPS FTP |
-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) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-B0W / |
#4: Chemical | ChemComp-IMP / |
#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: 2.46 Å3/Da / Density % sol: 50 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10 mM BES buffer |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0403 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Sep 10, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0403 Å / Relative weight: 1 |
Reflection | Resolution: 1.9→38.7 Å / Num. obs: 74613 / % possible obs: 97.7 % / Redundancy: 4.7 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 13.6 |
Reflection shell | Resolution: 1.9→2 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.481 / Mean I/σ(I) obs: 3.4 / Num. unique obs: 10693 / % possible all: 97.1 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.9→38.7 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.969 / SU B: 5.184 / SU ML: 0.072 / Cross valid method: THROUGHOUT / ESU R: 0.106 / ESU R Free: 0.1 / 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 33.004 Å2
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Refinement step | Cycle: 1 / Resolution: 1.9→38.7 Å
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Refine LS restraints |
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