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Yorodumi- PDB-7s6u: Leishmania infantum Glycogen Synthase Kinase 3 beta bound to AZD5438 -
+Open data
-Basic information
Entry | Database: PDB / ID: 7s6u | ||||||||||||
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Title | Leishmania infantum Glycogen Synthase Kinase 3 beta bound to AZD5438 | ||||||||||||
Components | Glycogen synthase kinase 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: 1.74 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 AZD5438 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 | 7s6u.cif.gz | 155.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7s6u.ent.gz | 119.7 KB | Display | PDB format |
PDBx/mmJSON format | 7s6u.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7s6u_validation.pdf.gz | 784.5 KB | Display | wwPDB validaton report |
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Full document | 7s6u_full_validation.pdf.gz | 786.1 KB | Display | |
Data in XML | 7s6u_validation.xml.gz | 16.3 KB | Display | |
Data in CIF | 7s6u_validation.cif.gz | 23.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/s6/7s6u ftp://data.pdbj.org/pub/pdb/validation_reports/s6/7s6u | HTTPS FTP |
-Related structure data
Related structure data | 3e3pS 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-FB8 / | ||||||
#3: Chemical | #4: Chemical | ChemComp-CAC / | #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: 2.32 Å3/Da / Density % sol: 47.05 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6 Details: 20% PEG 3350, 0.2 M Sodium bromide, 10% Ethylene glycol, 0.1 M SSB (0.04 M Sodium propionate, 0.02 M Sodium cacodylate trihydrate and 0.04 M Bis-Tris propane) |
-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: Oct 22, 2020 |
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: 1.74→29.26 Å / Num. obs: 38529 / % possible obs: 98.8 % / Redundancy: 4.9 % / Biso Wilson estimate: 26.983 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.067 / Rpim(I) all: 0.033 / Rrim(I) all: 0.075 / Net I/σ(I): 11.4 |
Reflection shell | Resolution: 1.74→1.77 Å / Redundancy: 4.9 % / Rmerge(I) obs: 1.051 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 2106 / CC1/2: 0.514 / Rpim(I) all: 0.51 / Rrim(I) all: 1.173 / % possible all: 98.9 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3E3P Resolution: 1.74→29.26 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.963 / SU B: 5.035 / SU ML: 0.077 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.106 / ESU R Free: 0.101 / 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: 88.4 Å2 / Biso mean: 32.377 Å2 / Biso min: 18.79 Å2
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Refinement step | Cycle: final / Resolution: 1.74→29.26 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.74→1.785 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Origin x: 53.8061 Å / Origin y: 22.9359 Å / Origin z: 42.2632 Å
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