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- PDB-3bd6: Glycogen Phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bd6 | ||||||
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Title | Glycogen Phosphorylase complex with 1(-D-ribofuranosyl) cyanuric acid | ||||||
![]() | Glycogen phosphorylase, muscle form | ||||||
![]() | TRANSFERASE / glycogenolysis / type 2 diabetes / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphorylation / Pyridoxal phosphate | ||||||
Function / homology | ![]() 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 | ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Sovantzis, D.A. / Hadjiloi, T. / Hayes, J.M. / Zographos, S.E. / Chrysina, E.D. / Oikonomakos, N.G. | ||||||
![]() | ![]() Title: D-Glucopyranosyl pyrimidine nucleoside binding to muscle glycogen phosphorylase b Authors: Cisma, C. / Sovantzis, D.A. / Hadjiloi, T. / Stathis, D. / Gimisis, T. / Hayes, J.M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Oikonomakos, N.G. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181 KB | Display | ![]() |
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PDB format | ![]() | 141.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 767.3 KB | Display | ![]() |
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Full document | ![]() | 773.3 KB | Display | |
Data in XML | ![]() | 31.2 KB | Display | |
Data in CIF | ![]() | 44.7 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 3bcrC ![]() 3bcsC ![]() 3bcuC ![]() 3bd7C ![]() 3bd8C ![]() 3bdaC ![]() 2prjS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-RDD / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.47 Å3/Da / Density % sol: 50.16 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10mM Bes buffer, 3mM DDT, pH6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Oct 2, 2005 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2→30 Å / Num. all: 65282 / Num. obs: 65282 / % possible obs: 98.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Rsym value: 0.047 / Net I/σ(I): 18.6 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.9 % / Mean I/σ(I) obs: 4.5 / Rsym value: 0.435 / % possible all: 98.1 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 2PRJ Resolution: 2→21.58 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.956 / SU B: 3.444 / SU ML: 0.097 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.175 / ESU R Free: 0.14 / 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: 34.177 Å2
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Refinement step | Cycle: LAST / Resolution: 2→21.58 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.052 Å / Total num. of bins used: 20
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