+Open data
-Basic information
Entry | Database: PDB / ID: 4eky | ||||||
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Title | Crystal structure of GPb in complex with DK15 | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / alpha/beta protein | ||||||
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: 2.45 Å | ||||||
Authors | Kantsadi, A.L. / Skamnaki, V.T. / Leonidas, D.D. | ||||||
Citation | Journal: Eur.J.Med.Chem. / Year: 2012 Title: The binding of C5-alkynyl and alkylfurano[2,3-d]pyrimidine glucopyranonucleosides to glycogen phosphorylase b: Synthesis, biochemical and biological assessment. Authors: Kantsadi, A.L. / Manta, S. / Psarra, A.M. / Dimopoulou, A. / Kiritsis, C. / Parmenopoulou, V. / Skamnaki, V.T. / 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 | 4eky.cif.gz | 180.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4eky.ent.gz | 139.6 KB | Display | PDB format |
PDBx/mmJSON format | 4eky.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ek/4eky ftp://data.pdbj.org/pub/pdb/validation_reports/ek/4eky | HTTPS FTP |
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-Related structure data
Related structure data | 4ej2C 4ekeC 4el0C 4el5C 3symS 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
#1: Protein | Mass: 95509.031 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: Chemical | ChemComp-D1J / |
#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: 2.53 Å3/Da / Density % sol: 51.3 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10mM BES buffer, 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: 1.5419 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: Oct 7, 2011 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→13.7 Å / Num. all: 33602 / Num. obs: 33602 / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Rsym value: 0.109 / Net I/σ(I): 13.8 |
Reflection shell | Resolution: 2.45→2.58 Å / Redundancy: 4.1 % / Mean I/σ(I) obs: 2.3 / Num. unique all: 4314 / Rsym value: 0.491 / % possible all: 82.4 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 3SYM Resolution: 2.45→13.57 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.916 / SU B: 7.722 / SU ML: 0.176 / Cross valid method: THROUGHOUT / ESU R: 0.494 / ESU R Free: 0.272 / 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: 25.635 Å2
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Refinement step | Cycle: LAST / Resolution: 2.45→13.57 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.45→2.512 Å / Total num. of bins used: 20
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