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Yorodumi- PDB-3cej: Human glycogen phosphorylase (tense state) in complex with the al... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3cej | ||||||
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Title | Human glycogen phosphorylase (tense state) in complex with the allosteric inhibitor AVE2865 | ||||||
Components | Glycogen phosphorylase, liver form | ||||||
Keywords | TRANSFERASE / protein ligand complex / tense state / allosteric inhibitor / Allosteric enzyme / Carbohydrate metabolism / Disease mutation / Glycogen metabolism / Glycogen storage disease / Glycosyltransferase / Nucleotide-binding / Phosphoprotein / Pyridoxal phosphate | ||||||
Function / homology | Function and homology information vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding ...vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / glucose binding / glycogen phosphorylase / glycogen phosphorylase activity / linear malto-oligosaccharide phosphorylase activity / SHG alpha-glucan phosphorylase activity / glycogen catabolic process / bile acid binding / Glycogen breakdown (glycogenolysis) / glycogen metabolic process / AMP binding / necroptotic process / response to bacterium / pyridoxal phosphate binding / glucose homeostasis / secretory granule lumen / ficolin-1-rich granule lumen / Neutrophil degranulation / extracellular exosome / extracellular region / ATP binding / identical protein binding / cytosol / cytoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 3.3 Å | ||||||
Authors | Wendt, K.U. / Dreyer, M.K. / Anderka, O. / Klabunde, T. / Loenze, P. / Defossa, E. / Schmoll, D. | ||||||
Citation | Journal: Biochemistry / Year: 2008 Title: Thermodynamic characterization of allosteric glycogen phosphorylase inhibitors. Authors: Anderka, O. / Loenze, P. / Klabunde, T. / Dreyer, M.K. / Defossa, E. / Wendt, K.U. / Schmoll, D. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3cej.cif.gz | 317.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3cej.ent.gz | 261.6 KB | Display | PDB format |
PDBx/mmJSON format | 3cej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ce/3cej ftp://data.pdbj.org/pub/pdb/validation_reports/ce/3cej | HTTPS FTP |
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-Related 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: 93063.586 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: PYGL / Cell line (production host): Sf9 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P06737, glycogen phosphorylase #2: Sugar | #3: Chemical | #4: Chemical | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.87 Å3/Da / Density % sol: 57.18 % |
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Crystal grow | Method: vapor diffusion, hanging drop / pH: 6.5 Details: VAPOR DIFFUSION, HANGING DROP, 7 mg/ml in 20 mM BES, 1 mM EDTA, 0.5 mM DTT, pH 6.5, 50 mM NBG, 2.5 mM AVF (AVE2865) |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 3.3→20 Å / Num. obs: 25212 / % possible obs: 80.8 % |
-Processing
Software |
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Refinement | Resolution: 3.3→19.47 Å / Cor.coef. Fo:Fc: 0.925 / Cor.coef. Fo:Fc free: 0.807 / SU B: 28.423 / SU ML: 0.477 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.72 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 56.085 Å2
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Refinement step | Cycle: LAST / Resolution: 3.3→19.47 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 3.3→3.383 Å / Total num. of bins used: 20
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