+Open data
-Basic information
Entry | Database: PDB / ID: 3t3d | |||||||||
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Title | Glycogen phosphorylase b in complex with GlcU | |||||||||
Components | Glycogen phosphorylase, muscle form | |||||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / a+b protein / transferase / muscle / TRANSFERASE-TRANSFERASE INHIBITOR complex | |||||||||
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 | Kantsadi, A.L. / Skamnaki, V.T. / Leonidas, D.D. | |||||||||
Citation | Journal: Chemmedchem / Year: 2012 Title: The sigma-Hole Phenomenon of Halogen Atoms Forms the Structural Basis of the Strong Inhibitory Potency of C5 Halogen Substituted Glucopyranosyl Nucleosides towards Glycogen Phosphorylase b Authors: Kantsadi, A.L. / Hayes, J.M. / Manta, S. / Skamnaki, V.T. / Kiritsis, C. / Psarra, A.M. / Koutsogiannis, Z. / Dimopoulou, A. / Theofanous, S. / Nikoleousakos, N. / Zoumpoulakis, P. / Kontou, ...Authors: Kantsadi, A.L. / Hayes, J.M. / Manta, S. / Skamnaki, V.T. / Kiritsis, C. / Psarra, A.M. / Koutsogiannis, Z. / Dimopoulou, A. / Theofanous, S. / Nikoleousakos, N. / Zoumpoulakis, P. / Kontou, M. / Papadopoulos, G. / 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 | 3t3d.cif.gz | 180.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3t3d.ent.gz | 140.7 KB | Display | PDB format |
PDBx/mmJSON format | 3t3d.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3t3d_validation.pdf.gz | 745.1 KB | Display | wwPDB validaton report |
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Full document | 3t3d_full_validation.pdf.gz | 754.2 KB | Display | |
Data in XML | 3t3d_validation.xml.gz | 31.1 KB | Display | |
Data in CIF | 3t3d_validation.cif.gz | 44.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t3/3t3d ftp://data.pdbj.org/pub/pdb/validation_reports/t3/3t3d | HTTPS FTP |
-Related structure data
Related structure data | 3t3eC 3t3gC 3t3hC 3t3iC 2gpnS S: Starting model for refinement 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: 97519.320 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: Sugar | ChemComp-CJB / |
#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: 2.47 Å3/Da / Density % sol: 50.13 % |
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Crystal grow | Temperature: 289 K / Method: small tubes / pH: 6.7 Details: T state crystals soaked with 2 mM solution of the inhibitor in the crystallization media for 2hrs, 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: Apr 2, 2011 |
Radiation | Monochromator: mirror / 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→30 Å / Num. all: 33377 / Num. obs: 33377 / % possible obs: 97.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 8 % / Rmerge(I) obs: 0.108 / Net I/σ(I): 17.6 |
Reflection shell | Resolution: 2.5→2.64 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.478 / Mean I/σ(I) obs: 2.5 / Num. unique all: 4896 / % possible all: 99.2 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: PDB entry 2GPN Resolution: 2.5→13.77 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.917 / SU B: 7.725 / SU ML: 0.171 / Cross valid method: THROUGHOUT / ESU R Free: 0.266 / 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: 26.102 Å2
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Refinement step | Cycle: LAST / Resolution: 2.5→13.77 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.5→2.565 Å / Total num. of bins used: 20
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