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Yorodumi- PDB-1c8k: FLAVOPIRIDOL INHIBITS GLYCOGEN PHOSPHORYLASE BY BINDING AT THE IN... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1c8k | ||||||
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Title | FLAVOPIRIDOL INHIBITS GLYCOGEN PHOSPHORYLASE BY BINDING AT THE INHIBITOR SITE | ||||||
Components | PROTEIN (GLYCOGEN PHOSPHORYLASE) | ||||||
Keywords | TRANSFERASE / GLYCOGEN METABOLISM / GLYCOGEN PHOSPHORYLASE B / INHIBITION / INHIBITOR BINDING SITE / ANTITUMOUR AGENT | ||||||
Function / homology | Function and homology information glycogen phosphorylase / glycogen 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: 1.76 Å | ||||||
Authors | Oikonomakos, N.G. / Zographos, S.E. / Skamnaki, V.T. / Tsitsanou, K.E. / Johnson, L.N. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2000 Title: Flavopiridol inhibits glycogen phosphorylase by binding at the inhibitor site. Authors: Oikonomakos, N.G. / Schnier, J.B. / Zographos, S.E. / Skamnaki, V.T. / Tsitsanou, K.E. / Johnson, L.N. #1: Journal: Protein Sci. / Year: 1999 Title: Allosteric Inhibition of Glycogen Phosphorylase a by the Potential Antidiabetic Drug 3-Isopropyl 4-(2-Chlorophenyl)-1,4-Dihydro-1-Ethyl-2-Methyl-Pyridine-3,5,6-Tricarboxylate Authors: Oikonomakos, N.G. / Tsitsanou, K.E. / Zographos, S.E. / Skamnaki, V.T. / Goldmann, S. / Bischoff, H. #2: 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. | ||||||
History |
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Remark 300 | DIMER IS THE PHYSIOLOGICALLY ACTIVE MOLECULE |
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1c8k.cif.gz | 186 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1c8k.ent.gz | 146.2 KB | Display | PDB format |
PDBx/mmJSON format | 1c8k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1c8k_validation.pdf.gz | 485.7 KB | Display | wwPDB validaton report |
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Full document | 1c8k_full_validation.pdf.gz | 509.3 KB | Display | |
Data in XML | 1c8k_validation.xml.gz | 19.6 KB | Display | |
Data in CIF | 1c8k_validation.cif.gz | 31.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c8/1c8k ftp://data.pdbj.org/pub/pdb/validation_reports/c8/1c8k | HTTPS FTP |
-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: 97291.203 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: MUSCLE / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-CPB / |
#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: 2.46 Å3/Da / Density % sol: 48 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | pH: 6.7 / Details: pH 6.70 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS pH: 6.7 / Method: other | ||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X31 / Wavelength: 1.05 |
Detector | Date: Mar 1, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.76→29.5 Å / Num. obs: 95442 / % possible obs: 99.3 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 14.6 |
Reflection shell | Resolution: 1.76→1.79 Å / Rmerge(I) obs: 0.64 / Mean I/σ(I) obs: 2 / % possible all: 97.5 |
Reflection | *PLUS Redundancy: 4.2 % / Num. measured all: 489494 |
Reflection shell | *PLUS % possible obs: 97.5 % / Rmerge(I) obs: 0.64 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 1.76→29.5 Å / Cross valid method: R FREE / σ(F): 0
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Refinement step | Cycle: LAST / Resolution: 1.76→29.5 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.8 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement | *PLUS Lowest resolution: 29.5 Å / Num. reflection Rfree: 4780 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints | *PLUS
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LS refinement shell | *PLUS Rfactor Rfree: 0.336 / Rfactor obs: 0.338 |