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Yorodumi- PDB-3npa: Glycogen phosphorylase complexed with 2,5-dihydroxy-4-(beta-D-glu... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3npa | |||||||||
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Title | Glycogen phosphorylase complexed with 2,5-dihydroxy-4-(beta-D-glucopyranosyl)-bromo-benzene | |||||||||
Components | Glycogen phosphorylase, muscle form | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / Glycogenolysis / type 2 diabetes / TRANSFERASE-TRANSFERASE 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 / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.969 Å | |||||||||
Authors | Alexacou, K.-M. | |||||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2011 Title: Halogen-substituted (C-beta-D-glucopyranosyl)-hydroquinone regioisomers: synthesis, enzymatic evaluation and their binding to glycogen phosphorylase. Authors: Alexacou, K.M. / Zhang, Y.Z. / Praly, J.P. / Zographos, S.E. / Chrysina, E.D. / Oikonomakos, N.G. / Leonidas, D.D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3npa.cif.gz | 182.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3npa.ent.gz | 142.3 KB | Display | PDB format |
PDBx/mmJSON format | 3npa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/np/3npa ftp://data.pdbj.org/pub/pdb/validation_reports/np/3npa | HTTPS FTP |
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-Related structure data
Related structure data | 3np7C 3np9C 3s0jC 2prjS C: citing same article (ref.) S: Starting model for refinement |
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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 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 / Details: Muscle / Source: (natural) Oryctolagus cuniculus (rabbit) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Sugar | ChemComp-Z57 / ( |
#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: 2.47 Å3/Da / Density % sol: 50.25 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 20 mg/mL protein in a buffer consisting of 10 mM BES, 0.5 mM EDTA, 3 mM DTT. T-state GPb crystals soaked with 20 mM inhibitor for 6 hrs, pH 6.7, SMALL TUBES, temperature 289K |
-Data collection
Diffraction | Mean temperature: 298 K |
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Diffraction source | Source: SYNCHROTRON / Site: SRS / Beamline: PX10.1 / Wavelength: 1.488 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 24, 2005 |
Radiation | Monochromator: Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 |
Reflection | Resolution: 1.969→30 Å / Num. all: 64845 / Num. obs: 64845 / % possible obs: 93.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 26.5 Å2 / Rmerge(I) obs: 0.065 / Net I/σ(I): 11.3 |
Reflection shell | Resolution: 1.969→2 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.298 / Mean I/σ(I) obs: 4.2 / Num. unique all: 3109 / % possible all: 90 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB ENTRY 2PRJ Resolution: 1.969→30 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.947 / SU B: 3.278 / SU ML: 0.095 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / ESU R: 0.178 / ESU R Free: 0.147 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.836 Å2
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Refinement step | Cycle: LAST / Resolution: 1.969→30 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.969→2.02 Å / Total num. of bins used: 20
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