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Yorodumi- PDB-3zcu: Rabbit muscle glycogen phosphorylase b in complex with N-(pyridyl... -
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-Basic information
Entry | Database: PDB / ID: 3zcu | ||||||
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Title | Rabbit muscle glycogen phosphorylase b in complex with N-(pyridyl-2- carbonyl)-N-beta-D-glucopyranosyl urea determined at 2.05 A resolution | ||||||
Components | GLYCOGEN PHOSPHORYLASE, MUSCLE FORM | ||||||
Keywords | TRANSFERASE / N-ACYL-N-BETA-D-GLUCOPYRANOSYL UREAS / INHIBITORS / HYPOGLYCAEMIC AGENTS / STRUCTURE BASED LIGAND DESIGN | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.05 Å | ||||||
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. ...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. | ||||||
Citation | Journal: To be Published 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: Journal: Eur.J.Biochem. / Year: 2002 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3zcu.cif.gz | 180.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3zcu.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 3zcu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/zc/3zcu ftp://data.pdbj.org/pub/pdb/validation_reports/zc/3zcu | HTTPS FTP |
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-Related structure data
Related structure data | 3zcpC 3zcqC 3zcrC 3zcsC 3zctC 3zcvC 2qnbS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-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) ORYCTOLAGUS CUNICULUS (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Sugar | ChemComp-T68 / |
#3: Chemical | ChemComp-PLP / |
#4: 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: 2.5 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: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.8088 |
Detector | Type: MARRESEARCH SX-165 / Detector: CCD / Date: Feb 14, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8088 Å / Relative weight: 1 |
Reflection | Resolution: 2.05→30 Å / Num. obs: 61537 / % possible obs: 99 % / Observed criterion σ(I): 0 / Redundancy: 5.3 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 21.2 |
Reflection shell | Resolution: 2.05→2.09 Å / Redundancy: 5.3 % / Rmerge(I) obs: 0.42 / Mean I/σ(I) obs: 4.1 / % possible all: 99.1 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 2QNB Resolution: 2.05→24.08 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.946 / SU B: 3.828 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.183 / ESU R Free: 0.155 / 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, 252-260, 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: 32.039 Å2
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Refinement step | Cycle: LAST / Resolution: 2.05→24.08 Å
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Refine LS restraints |
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