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Yorodumi- PDB-6s4k: The crystal structure of glycogen phosphorylase in complex with 12 -
+Open data
-Basic information
Entry | Database: PDB / ID: 6s4k | ||||||
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Title | The crystal structure of glycogen phosphorylase in complex with 12 | ||||||
Components | Glycogen phosphorylase, muscle form | ||||||
Keywords | TRANSFERASE / phosphorylase / inhibitor / C-beta-D-glucopyranosyl thiazole | ||||||
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: 2.43 Å | ||||||
Authors | Kyriakis, E. / Solovou, T.G.A. / Papaioannou, O.S.E. / Skamnaki, V.T. / Leonidas, D.D. | ||||||
Citation | Journal: Bioorg.Med.Chem. / Year: 2020 Title: The architecture of hydrogen and sulfur sigma-hole interactions explain differences in the inhibitory potency of C-beta-d-glucopyranosyl thiazoles, imidazoles and an N-beta-d glucopyranosyl ...Title: The architecture of hydrogen and sulfur sigma-hole interactions explain differences in the inhibitory potency of C-beta-d-glucopyranosyl thiazoles, imidazoles and an N-beta-d glucopyranosyl tetrazole for human liver glycogen phosphorylase and offer new insights to structure-based design. Authors: Kyriakis, E. / Karra, A.G. / Papaioannou, O. / Solovou, T. / Skamnaki, V.T. / Liggri, P.G.V. / Zographos, S.E. / Szennyes, E. / Bokor, E. / Kun, S. / Psarra, A.G. / Somsak, L. / 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 | 6s4k.cif.gz | 333.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6s4k.ent.gz | 280 KB | Display | PDB format |
PDBx/mmJSON format | 6s4k.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s4/6s4k ftp://data.pdbj.org/pub/pdb/validation_reports/s4/6s4k | HTTPS FTP |
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-Related structure data
Related structure data | 6s4hC 6s4oC 6s4pC 6s4rC 6s51C 6s52C C: citing same article (ref.) |
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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: 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-KVW / ( |
#3: Chemical | ChemComp-PLP / |
#4: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.54 Å3/Da / Density % sol: 51.64 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 / Details: 10 mM BES buffer, pH 6.7 |
-Data collection
Diffraction | Mean temperature: 293 K / Serial crystal experiment: N |
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Diffraction source | Source: SEALED TUBE / Type: OXFORD DIFFRACTION SUPERNOVA / Wavelength: 1.5419 Å |
Detector | Type: AGILENT ATLAS CCD / Detector: CCD / Date: May 29, 2018 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 |
Reflection | Resolution: 2.43→13.52 Å / Num. obs: 32703 / % possible obs: 90 % / Redundancy: 5.9 % / CC1/2: 0.997 / Rsym value: 0.076 / Net I/σ(I): 16.5 |
Reflection shell | Resolution: 2.43→2.53 Å / Redundancy: 4.3 % / Mean I/σ(I) obs: 3.1 / Num. unique obs: 3151 / CC1/2: 0.901 / Rsym value: 0.419 / % possible all: 78.6 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 2.43→13.52 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.931 / SU B: 14.826 / SU ML: 0.165 / Cross valid method: THROUGHOUT / ESU R: 0.536 / ESU R Free: 0.255 / 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: 1.1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.161 Å2
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Refinement step | Cycle: LAST / Resolution: 2.43→13.52 Å
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Refine LS restraints |
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