+Open data
-Basic information
Entry | Database: PDB / ID: 3l7d | ||||||
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Title | Crystal Structure of Glycogen Phosphorylase DK5 complex | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / GLYCOGENOLYSIS / TYPE 2 DIABETES / allosteric enzyme / CARBOHYDRATE METABOLISM / GLYCOGEN METABOLISM / GLYCOSYLTRANSFERASE / NUCLEOTIDE-BINDING / PHOSPHORYLATION / PYRIDOXAL PHOSPHATE / Phosphoprotein | ||||||
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: 2 Å | ||||||
Authors | Tsirkone, V.G. / Lamprakis, C. / Hayes, J.M. / Skamnaki, V. / Drakou, C. / Zographos, S.E. / Leonidas, D.D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2010 Title: 1-(3-Deoxy-3-fluoro-beta-d-glucopyranosyl) pyrimidine derivatives as inhibitors of glycogen phosphorylase b: Kinetic, crystallographic and modelling studies. Authors: Tsirkone, V.G. / Tsoukala, E. / Lamprakis, C. / Manta, S. / Hayes, J.M. / Skamnaki, V.T. / Drakou, C. / Zographos, S.E. / Komiotis, D. / 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 | 3l7d.cif.gz | 183.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3l7d.ent.gz | 142 KB | Display | PDB format |
PDBx/mmJSON format | 3l7d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/l7/3l7d ftp://data.pdbj.org/pub/pdb/validation_reports/l7/3l7d | HTTPS FTP |
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-Related structure data
Related structure data | 3l79C 3l7aC 3l7bC 3l7cC 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: 97650.516 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-DK5 / |
#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: 2.5 Å3/Da / Density % sol: 50.75 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: 10MM BES BUFFER, 3MM DDT, pH 6.7, small tubes, temperature 289K |
-Data collection
Diffraction | Mean temperature: 289 K |
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Diffraction source | Source: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X13 / Wavelength: 0.81 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 29, 2009 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.81 Å / Relative weight: 1 |
Reflection | Resolution: 2→99 Å / Num. obs: 65604 / % possible obs: 97.5 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 5 % / Rmerge(I) obs: 0.051 / Χ2: 0.433 / Net I/σ(I): 4.9 |
Reflection shell | Resolution: 2→2.03 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.493 / Mean I/σ(I) obs: 2.2 / Num. unique all: 3272 / Χ2: 0.609 / % possible all: 98.3 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2PRJ Resolution: 2→49.27 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.169 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 72.42 Å2 / Biso mean: 31.109 Å2 / Biso min: 12.3 Å2
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Refinement step | Cycle: LAST / Resolution: 2→49.27 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2→2.051 Å / Total num. of bins used: 20
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