+Open data
-Basic information
Entry | Database: PDB / ID: 5jtt | ||||||
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Title | Crystal structure of GPb in complex with 8a | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / alpha and beta protein 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: 1.85 Å | ||||||
Authors | Kantsadi, A.L. / Stravodimos, G.A. / Chatzileontiadou, D.S.M. / Leonidas, D.D. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2016 Title: Synthetic, enzyme kinetic, and protein crystallographic studies of C-beta-d-glucopyranosyl pyrroles and imidazoles reveal and explain low nanomolar inhibition of human liver glycogen phosphorylase. Authors: Kantsadi, A.L. / Bokor, E. / Kun, S. / Stravodimos, G.A. / Chatzileontiadou, D.S. / Leonidas, D.D. / Juhasz-Toth, E. / Szakacs, A. / Batta, G. / Docsa, T. / Gergely, P. / Somsak, L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5jtt.cif.gz | 179.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5jtt.ent.gz | 146.3 KB | Display | PDB format |
PDBx/mmJSON format | 5jtt.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jt/5jtt ftp://data.pdbj.org/pub/pdb/validation_reports/jt/5jtt | 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 on special symmetry positions |
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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-6MY / ( |
#4: Chemical | ChemComp-DMS / |
#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: 2.56 Å3/Da / Density % sol: 51.99 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10mM 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 5, 2015 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0403 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→38.39 Å / Num. obs: 82598 / % possible obs: 99.3 % / Redundancy: 3.9 % / Rmerge(I) obs: 0.069 / Net I/σ(I): 12.2 |
Reflection shell | Resolution: 1.85→1.95 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.428 / Mean I/σ(I) obs: 3.3 / % possible all: 98.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 1.85→38.39 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.378 / SU ML: 0.071 / Cross valid method: THROUGHOUT / ESU R: 0.11 / ESU R Free: 0.105 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 30.89 Å2
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Refinement step | Cycle: LAST / Resolution: 1.85→38.39 Å
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Refine LS restraints |
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