+Open data
-Basic information
Entry | Database: PDB / ID: 4z5x | ||||||
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Title | Glycogen phosphorylase in complex with gallic acid | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / alpha and beta protein | ||||||
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: 2.1 Å | ||||||
Authors | Kyriakis, E. / Kantsadi, L.A. / Stravodimos, A.G. / Chatzileontiadou, S.M.D. / Leonidas, D.D. | ||||||
Citation | Journal: Febs Lett. / Year: 2015 Title: Natural flavonoids as antidiabetic agents. The binding of gallic and ellagic acids to glycogen phosphorylase b. Authors: Kyriakis, E. / Stravodimos, G.A. / Kantsadi, A.L. / Chatzileontiadou, D.S. / Skamnaki, V.T. / 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 | 4z5x.cif.gz | 176.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4z5x.ent.gz | 144.3 KB | Display | PDB format |
PDBx/mmJSON format | 4z5x.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4z5x_validation.pdf.gz | 459.1 KB | Display | wwPDB validaton report |
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Full document | 4z5x_full_validation.pdf.gz | 460.7 KB | Display | |
Data in XML | 4z5x_validation.xml.gz | 29.9 KB | Display | |
Data in CIF | 4z5x_validation.cif.gz | 43.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/z5/4z5x ftp://data.pdbj.org/pub/pdb/validation_reports/z5/4z5x | 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: 97438.398 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-GDE / |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION |
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-Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.2 % |
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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 |
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Diffraction source | Source: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P14 (MX2) / Wavelength: 1.04 Å |
Detector | Type: RAYONIX MX225HE / Detector: CCD / Date: Dec 7, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04 Å / Relative weight: 1 |
Reflection | Resolution: 2.1→86.36 Å / Num. obs: 56323 / % possible obs: 98.4 % / Redundancy: 6.7 % / Rsym value: 0.077 / Net I/σ(I): 15.4 |
Reflection shell | Resolution: 2.1→2.21 Å / Redundancy: 6.9 % / Mean I/σ(I) obs: 5.1 / % possible all: 97.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.1→90.85 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.886 / SU ML: 0.102 / Cross valid method: THROUGHOUT / ESU R: 0.175 / ESU R Free: 0.146 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 42.4 Å2
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Refinement step | Cycle: LAST / Resolution: 2.1→90.85 Å
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Refine LS restraints |
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