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Yorodumi- PDB-3sym: Glycogen Phosphorylase b in complex with 3 -C-(hydroxymethyl)-bet... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3sym | |||||||||
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Title | Glycogen Phosphorylase b in complex with 3 -C-(hydroxymethyl)-beta-D-glucopyranonucleoside of 5-fluorouracil | |||||||||
Components | Glycogen phosphorylase, muscle form | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / alpha and beta protein / TRANSFERASE-TRANSFERASE INHIBITOR complex / muscle / transferase / glycogen metabolism | |||||||||
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 / FOURIER SYNTHESIS / Resolution: 2.4 Å | |||||||||
Authors | Skamnaki, V.T. / Katsandi, A.L. / Kontou, M. / Leonidas, D.D. | |||||||||
Citation | Journal: Chem.Biol.Drug Des. / Year: 2012 Title: 3'-Axial CH(2) OH Substitution on Glucopyranose does not Increase Glycogen Phosphorylase Inhibitory Potency. QM/MM-PBSA Calculations Suggest Why. Authors: Manta, S. / Xipnitou, A. / Kiritsis, C. / Kantsadi, A.L. / Hayes, J.M. / Skamnaki, V.T. / Lamprakis, C. / Kontou, M. / Zoumpoulakis, P. / Zographos, S.E. / Leonidas, D.D. / Komiotis, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3sym.cif.gz | 174.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3sym.ent.gz | 140.9 KB | Display | PDB format |
PDBx/mmJSON format | 3sym.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/sy/3sym ftp://data.pdbj.org/pub/pdb/validation_reports/sy/3sym | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 97519.320 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Sugar | ChemComp-GP0 / |
#3: 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: 49.96 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 2mM INHIBITOR SOAKED WITH T-STATE NATIVE ENZYME CRYSTAL FOR 2 HRS, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 293 K |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION ENHANCE ULTRA / Wavelength: 1.5418 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Apr 2, 2011 |
Radiation | Monochromator: mirror / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→30 Å / Num. all: 38290 / Num. obs: 36321 / % possible obs: 99.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 4.7 % / Rsym value: 0.083 / Net I/σ(I): 14.9 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 3.1 % / Rmerge(I) obs: 0.489 / Mean I/σ(I) obs: 3.1 / % possible all: 98.8 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.4→13.86 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.934 / SU B: 6.494 / SU ML: 0.148 / Cross valid method: THROUGHOUT / ESU R: 0.344 / ESU R Free: 0.216 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.375 Å2
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Refinement step | Cycle: LAST / Resolution: 2.4→13.86 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.4→2.46 Å / Total num. of bins used: 20
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