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Yorodumi- PDB-1fs4: Structures of glycogen phosphorylase-inhibitor complexes and the ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1fs4 | ||||||
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Title | Structures of glycogen phosphorylase-inhibitor complexes and the implications for structure-based drug design | ||||||
Components | GLYCOGEN PHOSPHORYLASE | ||||||
Keywords | TRANSFERASE / enzyme-inhibitor complex | ||||||
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 / DIFFERENCE FOURIER METHODS / Resolution: 2.38 Å | ||||||
Authors | Watson, K.A. / Tsitsanou, K.E. / Gregoriou, M. / Zographos, S.E. / Skamnaki, V.T. / Oikonomakos, N.G. / Fleet, G.W. / Johnson, L.N. | ||||||
Citation | Journal: Proteins / Year: 2005 Title: Kinetic and crystallographic studies of glucopyranose spirohydantoin and glucopyranosylamine analogs inhibitors of glycogen phosphorylase. Authors: Watson, K.A. / Chrysina, E.D. / Tsitsanou, K.E. / Zographos, S.E. / Archontis, G. / Fleet, G.W. / Oikonomakos, N.G. #1: Journal: Protein Sci. / Year: 1998 Title: The Structure of a Glycogen Phosphorylase Glucopyranose Spirohydantoin Complex at 1.8 A Resolution and 100K: The Role of the Water Structure and its Contribution to Binding Authors: Gregoriou, M. / Noble, M.E. / Watson, K.A. / Garman, E.F. / Krulle, T.M. / de la Fuente, C. / Fleet, G.W. / Oikonomakos, N.G. / Johnson, L.N. #2: Journal: Tetrahedron Lett. / Year: 1995 Title: Potent Inhibition of Glycogen Phosphorylase by a Spirohydantoin of Glucopyranose: First Pyranose Analogues of Hydantocidin Authors: Bichard, C.J.F. / Mitchell, E.P. / Wormald, M.R. / Watson, K.A. / Johnson, L.N. / Zographos, S.E. / Koutra, D.D. / Oikonomakos, N.G. / Fleet, G.W.J. #3: Journal: Protein Sci. / Year: 1995 Title: N-Acetyl-Beta-D-Glucopyranosylamine: A Potent T-State Inhibitor of Glycogen Phosphorylase. A Comparison with Alpha-D-Glucose Authors: Oikonomakos, N.G. / Kontou, M. / Zographos, S.E. / Watson, K.A. / Johnson, L.N. / Bichard, C.J. / Fleet, G.W. / Acharya, K.R. #4: Journal: Biochemistry / Year: 1994 Title: Design of Inhibitors of Glycogen Phosphorylase: A Study of Alpha- and Beta-C-Glucosides and 1-Thio-Beta-D-Glucose Compounds Authors: Watson, K.A. / Mitchell, E.P. / Johnson, L.N. / Son, J.C. / Bichard, C.J. / Orchard, M.G. / Fleet, G.W. / Oikonomakos, N.G. / Leonidas, D.D. / Kontou, M. / Papageorgiou, A.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1fs4.cif.gz | 177.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1fs4.ent.gz | 144.5 KB | Display | PDB format |
PDBx/mmJSON format | 1fs4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1fs4_validation.pdf.gz | 470.6 KB | Display | wwPDB validaton report |
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Full document | 1fs4_full_validation.pdf.gz | 493.7 KB | Display | |
Data in XML | 1fs4_validation.xml.gz | 19.4 KB | Display | |
Data in CIF | 1fs4_validation.cif.gz | 30 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fs/1fs4 ftp://data.pdbj.org/pub/pdb/validation_reports/fs/1fs4 | HTTPS FTP |
-Related structure data
Related structure data | 1ftqC 1ftwC 1ftyC 1fu4C 1fu7C 1fu8C C: citing same article (ref.) |
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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: 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: Sugar | ChemComp-CRA / |
#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: 2.47 Å3/Da / Density % sol: 50.13 % | |||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: BES, EDTA, IMP, spermine, pH 6.7, SMALL TUBES, temperature 289K | |||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 16 ℃ / Method: unknownDetails: Oikonomakos, N.G., (1985) Biochim.Biophys.Acta., 832, 248. | |||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: NICOLET / Detector: AREA DETECTOR / Date: Apr 3, 1996 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.38→15.5 Å / Num. all: 32187 / % possible obs: 82 % / Rmerge(I) obs: 0.076 |
Reflection shell | Resolution: 2.38→2.49 Å |
Reflection | *PLUS Num. obs: 32187 / % possible obs: 82 % / Num. measured all: 145498 |
-Processing
Software |
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Refinement | Method to determine structure: DIFFERENCE FOURIER METHODS / Resolution: 2.38→15.5 Å / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.38→15.5 Å
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Refine LS restraints |
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Software | *PLUS Version: 3.851 / Classification: refinement | ||||||||||||||||
Refinement | *PLUS % reflection Rfree: 5 % / Rfactor obs: 0.177 / Rfactor Rfree: 0.224 | ||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||
Displacement parameters | *PLUS | ||||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 1.4 |