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- PDB-2qln: Glycogen Phosphorylase b in complex with N-4-phenylbenzoyl-N'-bet... -
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Open data
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Basic information
Entry | Database: PDB / ID: 2qln | ||||||
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Title | Glycogen Phosphorylase b in complex with N-4-phenylbenzoyl-N'-beta-D-glucopyranosyl urea | ||||||
![]() | Glycogen phosphorylase, muscle form | ||||||
![]() | TRANSFERASE / glycogenolysis / type 2 diabetes / Acetylation / Allosteric enzyme / Carbohydrate metabolism / Glycogen metabolism / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / 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 | ![]() ![]() ![]() | ||||||
![]() | Oikonomakos, N.G. / Chrysina, E.D. / Tiraidis, C. / Alexacou, K.-M. / Leonidas, D.D. / Sographos, S.E. | ||||||
![]() | ![]() Title: N-(4-substituted-benzoyl)-N'-(beta-D-glucopyranosyl)ureas, inhibitors of glycogen phosphorylase: synthesis, kinetic and crystallographic evaluation Authors: Nagy, V. / Felf ldi, N. / Praly, J.-P. / Dosca, T. / Gergerly, P. / Chrysina, E.D. / Tiraidis, C. / Kosmopoulou, M.N. / Alexacou, K.-M. / Konstantakaki, M. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.4 KB | Display | ![]() |
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PDB format | ![]() | 141.2 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 461 KB | Display | ![]() |
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Full document | ![]() | 463.9 KB | Display | |
Data in XML | ![]() | 16.1 KB | Display | |
Data in CIF | ![]() | 26.3 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 2qlmC ![]() 2qn3C ![]() 2qn7C ![]() 2qn8C ![]() 2qn9C ![]() 2qnbC ![]() 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 / Source: (natural) ![]() ![]() |
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#2: Chemical | ChemComp-F59 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.48 Å3/Da / Density % sol: 50.43 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10 mM Bes, 3 mM DDT, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Nov 20, 2004 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.813 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→30 Å / Num. all: 53808 / Num. obs: 53808 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 27.3 Å2 / Rsym value: 0.071 / Net I/σ(I): 18.1 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 7.6 % / Mean I/σ(I) obs: 6.2 / Num. unique all: 2632 / Rsym value: 0.367 / % possible all: 99.6 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB entry 2PRJ Resolution: 2.15→30 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.94 / SU B: 4.201 / SU ML: 0.112 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.215 / ESU R Free: 0.169 / 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: 26.805 Å2
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Refine analyze |
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Refinement step | Cycle: LAST / Resolution: 2.15→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.15→2.205 Å / Total num. of bins used: 20
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