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- PDB-3zcq: Rabbit muscle glycogen phosphorylase b in complex with N-(4- trif... -
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Open data
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Basic information
Entry | Database: PDB / ID: 3zcq | ||||||
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Title | Rabbit muscle glycogen phosphorylase b in complex with N-(4- trifluoromethyl-benzoyl)-N-beta-D-glucopyranosyl urea determined at 2. 15 A resolution | ||||||
![]() | GLYCOGEN PHOSPHORYLASE, MUSCLE FORM![]() | ||||||
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Function / homology | ![]() ![]() ![]() ![]() ![]() Similarity search - Function | ||||||
Biological species | ![]() ![]() ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Chrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. ...Chrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. / Konstantakaki, M. / Kardakaris, R. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. / Somsak, L. | ||||||
![]() | ![]() Title: Synthesis, Kinetic, Computational and Crystallographic Evaluation of N-Acyl-N-Beta-D- Glucopyranosyl)Ureas, Nanomolar Glucose Analogue Inhibitors of Glycogen Phosphorylase, Potential Antidiabetic Agents Authors: Chrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. / Konstantakaki, M. / Kardakaris, R. / Leonidas, D.D. ...Authors: Chrysina, E.D. / Nagy, V. / Felfoldi, N. / Konya, B. / Telepo, K. / Praly, J.P. / Docsa, T. / Gergely, P. / Alexacou, K.M. / Hayes, J.M. / Konstantakaki, M. / Kardakaris, R. / Leonidas, D.D. / Zographos, S.E. / Oikonomakos, N.G. / Somsak, L. #1: ![]() Title: Binding of N-Acetyl-N '-Beta-D-Glucopyranosyl Urea and N-Benzoyl-N '-Beta-D-Glucopyranosyl Urea to Glycogen Phosphorylase B: Kinetic and Crystallographic Studies. Authors: Oikonomakos, N.G. / Kosmopoulou, M. / Zographos, S.E. / Leonidas, D.D. / Chrysina, E.D. / Somsak, L. / Nagy, V. / Praly, J. / Docsa, T. / Toth, B. / Gergely, P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 181.2 KB | Display | ![]() |
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PDB format | ![]() | 141.8 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Arichive directory | ![]() ![]() | HTTPS FTP |
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-Related structure data
Related structure data | ![]() 3zcpC ![]() 3zcrC ![]() 3zcsC ![]() 3zctC ![]() 3zcuC ![]() 3zcvC ![]() 2qnbS 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: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Details: RABBIT SKELETAL MUSCLE / Source: (natural) ![]() ![]() ![]() ![]() ![]() |
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#2: Chemical | ChemComp-PLP / ![]() |
#3: Chemical | ChemComp-62N / |
#4: Chemical | ChemComp-PO4 / ![]() |
#5: Water | ChemComp-HOH / ![]() |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.5 Å3/Da / Density % sol: 50.7 % / Description: NONE |
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Crystal grow![]() | pH: 6.8 / Details: pH 6.8 |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 9, 2006 |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength![]() |
Reflection | Resolution: 2.15→30 Å / Num. obs: 53088 / % possible obs: 98.5 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 16.8 |
Reflection shell | Resolution: 2.15→2.19 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 5.1 / % possible all: 99.5 |
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Processing
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Refinement | Method to determine structure![]() ![]() Starting model: PDB ENTRY 2QNB Resolution: 2.15→29.59 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.939 / SU B: 4.362 / SU ML: 0.116 / Cross valid method: THROUGHOUT / ESU R: 0.22 / ESU R Free: 0.177 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE FOLLOWING RESIDUES WERE NOT INCLUDED IN THE STRUCTURE SINCE THERE WAS NOT SUFFICIENT DENSITY TO INDICATE THEIR POSITION 1-11, 252-257, 315-323, 837-842
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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: 30.528 Å2
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Refinement step | Cycle: LAST / Resolution: 2.15→29.59 Å
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Refine LS restraints |
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