+Open data
-Basic information
Entry | Database: PDB / ID: 2ati | ||||||
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Title | Glycogen Phosphorylase Inhibitors | ||||||
Components | Glycogen phosphorylase, liver form | ||||||
Keywords | TRANSFERASE / Glycogen Phosphorylase | ||||||
Function / homology | Function and homology information vitamin binding / purine nucleobase binding / 5-phosphoribose 1-diphosphate biosynthetic process / D-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 / D-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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.9 Å | ||||||
Authors | Klabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.J. / Herling, A.W. / Oikonomakos, N.G. / Schmoll, D. / Sarubbi, E. / von Roedern, E. ...Klabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.J. / Herling, A.W. / Oikonomakos, N.G. / Schmoll, D. / Sarubbi, E. / von Roedern, E. / Schoenafinger, K. / Defossa, E. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2005 Title: Acyl ureas as human liver glycogen phosphorylase inhibitors for the treatment of type 2 diabetes. Authors: Klabunde, T. / Wendt, K.U. / Kadereit, D. / Brachvogel, V. / Burger, H.J. / Herling, A.W. / Oikonomakos, N.G. / Kosmopoulou, M.N. / Schmoll, D. / Sarubbi, E. / von Roedern, E. / Defossa, E. #1: Journal: Protein Sci. / Year: 2005 Title: Crystallographic studies on acyl ureas, a new class of glycogen phosphorylase inhibitors, as potential antidiabetic drugs Authors: Oikonomakos, N.G. / Kosmopoulou, M.N. / Chrysina, E.D. / Leonidas, D.D. / Kostas, I.D. / Wendt, K.U. / Klabunde, T. / Defossa, E. #2: Journal: Mol.Cell / Year: 2000 Title: Activation of human liver glycogen phosphorylase by alteration of the secondary structure and packing of the catalytic core Authors: Rath, V.L. / Ammirati, M. / LeMotte, P.K. / Fennell, K.F. / Mansour, M.N. / Danley, D.E. / Hynes, T.R. / Schulte, G.K. / Wasilko, D.J. / Pandit, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2ati.cif.gz | 339.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2ati.ent.gz | 275.9 KB | Display | PDB format |
PDBx/mmJSON format | 2ati.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2ati_validation.pdf.gz | 548.6 KB | Display | wwPDB validaton report |
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Full document | 2ati_full_validation.pdf.gz | 558.1 KB | Display | |
Data in XML | 2ati_validation.xml.gz | 29.8 KB | Display | |
Data in CIF | 2ati_validation.cif.gz | 50.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/at/2ati ftp://data.pdbj.org/pub/pdb/validation_reports/at/2ati | HTTPS FTP |
-Related structure data
Related structure data | |
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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: 97145.266 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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: 2.84 Å3/Da / Density % sol: 56.63 % |
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID14-2 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Relative weight: 1 |
Reflection | Resolution: 1.9→500 Å / Num. all: 168283 / Num. obs: 167664 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 |
Reflection shell | Resolution: 1.9→2 Å / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Highest resolution: 1.9 Å / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Highest resolution: 1.9 Å
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