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Yorodumi- PDB-8bzs: The crystal structure of glycogen phosphorylase in complex with b... -
+Open data
-Basic information
Entry | Database: PDB / ID: 8bzs | ||||||
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Title | The crystal structure of glycogen phosphorylase in complex with baicalein | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.25 Å | ||||||
Authors | Koulas, S.M. / Mathomes, R. / Hayes, J.M. / Leonidas, D.D. | ||||||
Funding support | 1items
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Citation | Journal: Chem.Biol.Interact. / Year: 2023 Title: Multidisciplinary docking, kinetics and X-ray crystallography studies of baicalein acting as a glycogen phosphorylase inhibitor and determination of its' potential against glioblastoma in cellular models. Authors: Mathomes, R.T. / Koulas, S.M. / Tsialtas, I. / Stravodimos, G. / Welsby, P.J. / Psarra, A.G. / Stasik, I. / Leonidas, D.D. / Hayes, J.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8bzs.cif.gz | 335.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8bzs.ent.gz | 271.8 KB | Display | PDB format |
PDBx/mmJSON format | 8bzs.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bz/8bzs ftp://data.pdbj.org/pub/pdb/validation_reports/bz/8bzs | HTTPS FTP |
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-Related structure data
Related structure data | 6r0hS S: Starting model for refinement |
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Similar structure data | Similarity search - Function & homologyF&H Search |
-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) / References: UniProt: P00489, glycogen phosphorylase |
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#2: Chemical | ChemComp-PLP / |
#3: Chemical | ChemComp-3WL / |
#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: 2.57 Å3/Da / Density % sol: 52.19 % |
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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: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.54179 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Nov 5, 2020 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54179 Å / Relative weight: 1 |
Reflection | Resolution: 2.25→51.6 Å / Num. obs: 45448 / % possible obs: 97.5 % / Redundancy: 3.8 % / CC1/2: 0.984 / Rmerge(I) obs: 0.132 / Net I/σ(I): 6.3 |
Reflection shell | Resolution: 2.25→2.32 Å / Num. unique obs: 3980 / CC1/2: 0.669 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6R0H Resolution: 2.25→51.6 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.951 / SU B: 11.9 / SU ML: 0.139 / Cross valid method: THROUGHOUT / ESU R: 0.229 / ESU R Free: 0.186 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
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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 mean: 40.704 Å2
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Refinement step | Cycle: 1 / Resolution: 2.25→51.6 Å
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Refine LS restraints |
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