+Open data
-Basic information
Entry | Database: PDB / ID: 6r0h | ||||||
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Title | Glycogen Phosphorylase b in complex with 3 | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE | ||||||
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: 2.5 Å | ||||||
Authors | Tsagkarakou, S.A. / Koulas, M.S. / Kyriakis, E. / Stravodimos, G.A. / Skamnaki, V.T. / Leonidas, D.D. | ||||||
Citation | Journal: Molecules / Year: 2019 Title: High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-beta-d- ...Title: High Consistency of Structure-Based Design and X-Ray Crystallography: Design, Synthesis, Kinetic Evaluation and Crystallographic Binding Mode Determination of Biphenyl-N-acyl-beta-d-Glucopyranosylamines as Glycogen Phosphorylase Inhibitors. Authors: Fischer, T. / Koulas, S.M. / Tsagkarakou, A.S. / Kyriakis, E. / Stravodimos, G.A. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Riedl, R. / 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 | 6r0h.cif.gz | 334.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6r0h.ent.gz | 281.4 KB | Display | PDB format |
PDBx/mmJSON format | 6r0h.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r0/6r0h ftp://data.pdbj.org/pub/pdb/validation_reports/r0/6r0h | 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: 97422.398 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Oryctolagus cuniculus (rabbit) / Tissue: muscleSkeletal muscle / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-JN2 / |
#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: 2.45 Å3/Da / Density % sol: 49.84 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.8 / Details: 10 mM BES buffer |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION NOVA / Wavelength: 1.5419 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: May 10, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.5→13.71 Å / Num. obs: 32589 / % possible obs: 96.1 % / Redundancy: 3.7 % / CC1/2: 0.977 / Rsym value: 0.11 / Net I/σ(I): 10.3 |
Reflection shell | Resolution: 2.5→2.61 Å / Redundancy: 2.6 % / Mean I/σ(I) obs: 1.6 / Num. unique obs: 3644 / CC1/2: 0.563 / Rsym value: 0.754 / % possible all: 89.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.5→13.71 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.93 / SU B: 19.56 / SU ML: 0.2 / Cross valid method: THROUGHOUT / ESU R: 0.568 / ESU R Free: 0.258 / 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 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 29.439 Å2
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Refinement step | Cycle: 1 / Resolution: 2.5→13.71 Å
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Refine LS restraints |
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