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Yorodumi- PDB-7s6v: Leishmania infantum Glycogen Synthase Kinase 3 beta bound to CGP60474 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s6v | ||||||||||||
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Title | Leishmania infantum Glycogen Synthase Kinase 3 beta bound to CGP60474 | ||||||||||||
Components | Glycogen synthase kinase 3GSK-3 | ||||||||||||
Keywords | TRANSFERASE/INHIBITOR / Protein kinase / inhibitor / TRANSFERASE / GSK3s / GSK3beta / Leishmania infantum / TRANSFERASE-INHIBITOR complex | ||||||||||||
Function / homology | Function and homology information non-specific serine/threonine protein kinase / protein phosphorylation / protein serine/threonine kinase activity / ATP binding Similarity search - Function | ||||||||||||
Biological species | Leishmania infantum (eukaryote) | ||||||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.66 Å | ||||||||||||
Authors | dos Reis, C.V. / Ramos, P.Z. / Counago, R.M. | ||||||||||||
Funding support | Brazil, 3items
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Citation | Journal: To Be Published Title: Leishmania infantum Glycogen Synthase Kinase 3 beta bound to CGP60474 Authors: Ramos, P.Z. / dos Reis, C.V. / Counago, R.M. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7s6v.cif.gz | 152.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s6v.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 7s6v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/7s6v ftp://data.pdbj.org/pub/pdb/validation_reports/s6/7s6v | HTTPS FTP |
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-Related structure data
Related structure data | 7s6uS 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: 40933.863 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: GSK3, LINF_180007700, LINJ_18_0270 / Production host: Escherichia coli (E. coli) References: UniProt: A4HXQ3, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-8II / |
#3: Chemical | ChemComp-EDO / |
#4: Chemical | ChemComp-SO4 / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | N |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.34 Å3/Da / Density % sol: 47.52 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5 Details: PEG3350 20%, 300 mM Li2SO4, 100 mM SBG (42.8 mM Sodium tartrate dihydrate, 28.6 mM Bis-Tris and 28.6 mM Glycylglycine) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-E / Wavelength: 0.97918 Å |
Detector | Type: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Aug 6, 2021 |
Radiation | Monochromator: Cryogenically-cooled single crystal Si(220) side bounce Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97918 Å / Relative weight: 1 |
Reflection | Resolution: 1.66→76.62 Å / Num. obs: 44340 / % possible obs: 98.6 % / Redundancy: 6.1 % / CC1/2: 0.999 / Rmerge(I) obs: 0.058 / Rpim(I) all: 0.025 / Rrim(I) all: 0.063 / Net I/σ(I): 15.8 |
Reflection shell | Resolution: 1.66→1.69 Å / Rmerge(I) obs: 0.793 / Mean I/σ(I) obs: 2.1 / Num. unique obs: 1896 / CC1/2: 0.695 / Rpim(I) all: 0.356 / Rrim(I) all: 0.873 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7S6U Resolution: 1.66→76.62 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.949 / SU B: 3.912 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.097 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
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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: 85.81 Å2 / Biso mean: 26.431 Å2 / Biso min: 13.49 Å2
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Refinement step | Cycle: final / Resolution: 1.66→76.62 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.663→1.706 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 53.583 Å / Origin y: 23.206 Å / Origin z: 42.08 Å
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