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Yorodumi- PDB-6y55: The crystal structure of glycogen phosphorylase in complex with 43 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6y55 | ||||||
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Title | The crystal structure of glycogen phosphorylase in complex with 43 | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / glycogen metabolism | ||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen 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 / FOURIER SYNTHESIS / Resolution: 2.38 Å | ||||||
Authors | Kyriakis, E. / Koulas, S.M. / Skamnaki, V.T. / Leonidas, D.D. | ||||||
Citation | Journal: Bioorg.Chem. / Year: 2020 Title: Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ...Title: Synthetic flavonoid derivatives targeting the glycogen phosphorylase inhibitor site: QM/MM-PBSA motivated synthesis of substituted 5,7-dihydroxyflavones, crystallography, in vitro kinetics and ex-vivo cellular experiments reveal novel potent inhibitors. Authors: Chetter, B.A. / Kyriakis, E. / Barr, D. / Karra, A.G. / Katsidou, E. / Koulas, S.M. / Skamnaki, V.T. / Snape, T.J. / Psarra, A.G. / Leonidas, D.D. / 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 | 6y55.cif.gz | 331.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6y55.ent.gz | 277.7 KB | Display | PDB format |
PDBx/mmJSON format | 6y55.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6y55_validation.pdf.gz | 700.2 KB | Display | wwPDB validaton report |
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Full document | 6y55_full_validation.pdf.gz | 704.2 KB | Display | |
Data in XML | 6y55_validation.xml.gz | 30 KB | Display | |
Data in CIF | 6y55_validation.cif.gz | 43 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/y5/6y55 ftp://data.pdbj.org/pub/pdb/validation_reports/y5/6y55 | 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: 97650.516 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-O9Q / |
#3: 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: 2.42 Å3/Da / Density % sol: 49.2 % |
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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 / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.5419 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 30, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→13.67 Å / Num. obs: 34581 / % possible obs: 90.1 % / Redundancy: 5.8 % / CC1/2: 0.995 / Rmerge(I) obs: 0.095 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.38→2.47 Å / Redundancy: 4.3 % / Rmerge(I) obs: 0.57 / Mean I/σ(I) obs: 1.9 / Num. unique obs: 3009 / CC1/2: 0.84 / % possible all: 75.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.38→13.67 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.93 / SU B: 15.182 / SU ML: 0.168 / Cross valid method: THROUGHOUT / ESU R: 0.445 / ESU R Free: 0.243 / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.408 Å2
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Refinement step | Cycle: 1 / Resolution: 2.38→13.67 Å
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Refine LS restraints |
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