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- PDB-3bd8: Glucogen Phosphorylase complex with 1(-D-glucopyranosyl) cytosine -
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Open data
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Basic information
Entry | Database: PDB / ID: 3bd8 | |||||||||
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Title | Glucogen Phosphorylase complex with 1(-D-glucopyranosyl) cytosine | |||||||||
![]() | Glycogen phosphorylase, muscle form![]() | |||||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() 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 | ![]() | 181.5 KB | Display | ![]() |
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PDB format | ![]() | 142.4 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3bcrC ![]() 3bcsC ![]() 3bcuC ![]() 3bd6C ![]() 3bd7C ![]() 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: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: Muscle / Source: (natural) ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PLP / ![]() |
#3: Sugar | ChemComp-C3B / |
#4: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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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: 6.7 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: Feb 18, 2005 |
Radiation | Monochromator: crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.1→30 Å / Num. all: 57366 / Num. obs: 57366 / % possible obs: 99.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.2 % / Rsym value: 0.084 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 2.1→2.14 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.7 / Rsym value: 0.49 / % possible all: 99.6 |
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Processing
Software |
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2PRJ Resolution: 2.1→29.49 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Refinement step | Cycle: LAST / Resolution: 2.1→29.49 Å
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LS refinement shell | Resolution: 2.1→2.14 Å /
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