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Yorodumi- PDB-2off: The crystal structure of Glycogen Phosphorylase b in complex with... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2off | ||||||
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Title | The crystal structure of Glycogen Phosphorylase b in complex with a potent allosteric inhibitor | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / Glycogenolysis / type 2 diabetes | ||||||
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: 2.2 Å | ||||||
Authors | Tiraidis, C. / Alexacou, K.-M. / Zographos, S.E. / Leonidas, D.D. / Gimisis, T. / Oikonomakos, N.G. | ||||||
Citation | Journal: Protein Sci. / Year: 2007 Title: FR258900, a potential anti-hyperglycemic drug, binds at the allosteric site of glycogen phosphorylase Authors: Tiraidis, C. / Alexacou, K.-M. / Zographos, S.E. / Leonidas, D.D. / Gimisis, T. / Oikonomakos, N.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2off.cif.gz | 181.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2off.ent.gz | 141.8 KB | Display | PDB format |
PDBx/mmJSON format | 2off.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/of/2off ftp://data.pdbj.org/pub/pdb/validation_reports/of/2off | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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Details | Coordinates for a complete multimer representing the known biologically significant oligomerization state of the molecule can be generated by applying the transformations below: x,y,z and y,x,1-z |
-Components
#1: Protein | Mass: 97519.320 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-OFF / |
#3: 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: 2.47 Å3/Da / Density % sol: 50.12 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: Bes 10mM, EDTA, DTT, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX14.1 / Wavelength: 1.488 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 9, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→90.9 Å / Num. all: 48704 / Num. obs: 48704 / % possible obs: 97.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 6.3 % / Biso Wilson estimate: 32.592 Å2 / Rsym value: 0.107 / Net I/σ(I): 11.1 |
Reflection shell | Resolution: 2.2→2.24 Å / Redundancy: 6.5 % / Mean I/σ(I) obs: 4.7 / Rsym value: 0.431 / % possible all: 95.5 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.2→90.9 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.859 / SU ML: 0.126 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.255 / ESU R Free: 0.187 / 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: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 31.392 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.2→90.9 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.256 Å / Total num. of bins used: 20
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