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Yorodumi- PDB-7onf: The binding of p-coumaroyl glucose to glycogen phosphorylase reve... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7onf | ||||||
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Title | The binding of p-coumaroyl glucose to glycogen phosphorylase reveals the relationship between structural data and effects on cell metabolome | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.6 Å | ||||||
Authors | Tsagkarakou, A.S. / Koulas, S.M. / Kyriakis, E. / Drakou, C.E. / Leonidas, D.D. | ||||||
Citation | Journal: Eur J Med Chem Rep / Year: 2021 Title: Structure activity relationship of the binding of p-coumaroyl glucose to glycogen phosphorylase and its effect on hepatic cell metabolic pathways Authors: Tsagkarakou, A.S. / Chasapi, S.A. / Koulas, S.M. / Tsialtas, I. / Kyriakis, E. / Drakou, C.E. / Kun, S. / Somsak, L. / Spyroulias, G.A. / Psarra, A.M.G. / 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 | 7onf.cif.gz | 368.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7onf.ent.gz | 295.4 KB | Display | PDB format |
PDBx/mmJSON format | 7onf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7onf_validation.pdf.gz | 1.1 MB | Display | wwPDB validaton report |
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Full document | 7onf_full_validation.pdf.gz | 1.1 MB | Display | |
Data in XML | 7onf_validation.xml.gz | 32.3 KB | Display | |
Data in CIF | 7onf_validation.cif.gz | 48.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/on/7onf ftp://data.pdbj.org/pub/pdb/validation_reports/on/7onf | HTTPS FTP |
-Related structure data
Related structure data | 7o8e S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 95280.914 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: Muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-IMP / |
#4: Chemical | ChemComp-VKK / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.31 % |
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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: 298 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.9763 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 14, 2019 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9763 Å / Relative weight: 1 |
Reflection | Resolution: 1.6→86.4 Å / Num. obs: 128346 / % possible obs: 99.9 % / Redundancy: 6.5 % / Biso Wilson estimate: 28.2 Å2 / CC1/2: 0.998 / Net I/σ(I): 15.1 |
Reflection shell | Resolution: 1.6→1.63 Å / Rmerge(I) obs: 0.621 / Num. unique obs: 6280 / CC1/2: 0.9 / % possible all: 99.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7O8E 7o8e Resolution: 1.6→64.39 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.974 / SU B: 3.425 / SU ML: 0.049 / Cross valid method: THROUGHOUT / ESU R: 0.074 / ESU R Free: 0.064 / Stereochemistry target values: MAXIMUM LIKELIHOOD / 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 36.348 Å2
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Refinement step | Cycle: LAST / Resolution: 1.6→64.39 Å
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Refine LS restraints |
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