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Yorodumi- PDB-2amv: THE STRUCTURE OF GLYCOGEN PHOSPHORYLASE B WITH AN ALKYL-DIHYDROPY... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2amv | |||||||||
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Title | THE STRUCTURE OF GLYCOGEN PHOSPHORYLASE B WITH AN ALKYL-DIHYDROPYRIDINE-DICARBOXYLIC ACID | |||||||||
Components | PROTEIN (GLYCOGEN PHOSPHORYLASE) | |||||||||
Keywords | TRANSFERASE / GLYCOGEN PHOSPHORYLASE / GLYCOGEN METABOLISM / DIABETES / INHIBITORS / GLYCOSYLTRANSFERASE | |||||||||
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 / OTHER / Resolution: 2.3 Å | |||||||||
Authors | Zographos, S.E. / Oikonomakos, N.G. / Johnson, L.N. | |||||||||
Citation | Journal: Structure / Year: 1997 Title: The structure of glycogen phosphorylase b with an alkyldihydropyridine-dicarboxylic acid compound, a novel and potent inhibitor. Authors: Zographos, S.E. / Oikonomakos, N.G. / Tsitsanou, K.E. / Leonidas, D.D. / Chrysina, E.D. / Skamnaki, V.T. / Bischoff, H. / Goldmann, S. / Watson, K.A. / Johnson, L.N. #1: Journal: Protein Sci. / Year: 1999 Title: Effects of Commonly Used Cryoprotectants on Glycogen Phosphorylase Activity and Structure Authors: Tsitsanou, K.E. / Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Gregoriou, M. / Watson, K.A. / Johnson, L.N. / Fleet, G.W. #2: Journal: Glycogen Phosphorylase B: Description of the Protein Structure Year: 1991 Title: Glycogen Phosphorylase B: Description of the Protein Structure Authors: Acharya, K.R. / Stuart, D.I. / Varvill, K.M. / Johnson, L.N. #3: Journal: J.Mol.Biol. / Year: 1993 Title: Crystallographic Binding Studies on the Allosteric Inhibitor Glucose-6- Phosphate to T State Glycogen Phosphorylase b Authors: Johnson, L.N. / Snape, P. / Martin, J.L. / Acharya, K.R. / Barford, D. / Oikonomakos, N.G. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2amv.cif.gz | 187.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2amv.ent.gz | 154.5 KB | Display | PDB format |
PDBx/mmJSON format | 2amv.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/am/2amv ftp://data.pdbj.org/pub/pdb/validation_reports/am/2amv | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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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 / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLESkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-BIN / |
#4: Chemical | ChemComp-GOL / |
#5: 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: 2.4 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / pH: 6.7 Details: PHOSPHORYLASE B WAS COCRYSTALLISED WITH 1 MM W1807 IN A MEDIUM CONSISTING OF 27-28 MG/ML ENZYME, 1 MM SPERMINE, 3 MM DTT, 10 MM BES, 0.1 MM EDTA, AND 0.02% SODIUM AZIDE, PH 6.7 (16 DEG C)., temperature 289K | ||||||||||||||||||||||||||||||||||||||||
Crystal | *PLUS | ||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknown | ||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, Hamburg / Beamline: X11 / Wavelength: 0.928 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Nov 15, 1995 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.928 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→30 Å / Num. obs: 39549 / % possible obs: 94.9 % / Observed criterion σ(I): 0 / Redundancy: 6.1 % / Rmerge(I) obs: 0.095 / Net I/σ(I): 10.5 |
Reflection shell | Resolution: 2.3→2.38 Å / Rmerge(I) obs: 0.382 / Mean I/σ(I) obs: 3.6 / % possible all: 95.9 |
Reflection | *PLUS Num. measured all: 242759 |
Reflection shell | *PLUS % possible obs: 95.9 % |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.3→30 Å / Cross valid method: R FREE / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 2.3→30 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Highest resolution: 2.3 Å / Lowest resolution: 30 Å / σ(F): 0 / % reflection Rfree: 5 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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