+Open data
-Basic information
Entry | Database: PDB / ID: 8t5g | ||||||
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Title | SOS2 co-crystal structure with fragment bound (compound 12) | ||||||
Components | Son of sevenless homolog 2 | ||||||
Keywords | SIGNALING PROTEIN | ||||||
Function / homology | Function and homology information regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity ...regulation of pro-B cell differentiation / regulation of T cell differentiation in thymus / positive regulation of small GTPase mediated signal transduction / Interleukin-15 signaling / Activation of RAC1 / NRAGE signals death through JNK / regulation of T cell proliferation / B cell homeostasis / RAC1 GTPase cycle / guanyl-nucleotide exchange factor activity / G alpha (12/13) signalling events / insulin receptor signaling pathway / Ras protein signal transduction / protein heterodimerization activity / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å | ||||||
Authors | Gunn, R.J. / Lawson, J.D. / Ivetac, A. / Ulaganathan, T. / Coulombe, R. / Fethiere, J. | ||||||
Funding support | United States, 1items
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Citation | Journal: J.Med.Chem. / Year: 2024 Title: Discovery of Five SOS2 Fragment Hits with Binding Modes Determined by SOS2 X-Ray Cocrystallography. Authors: Smith, C.R. / Chen, D. / Christensen, J.G. / Coulombe, R. / Fethiere, J. / Gunn, R.J. / Hollander, J. / Jones, B. / Ketcham, J.M. / Khare, S. / Kuehler, J. / Lawson, J.D. / Marx, M.A. / ...Authors: Smith, C.R. / Chen, D. / Christensen, J.G. / Coulombe, R. / Fethiere, J. / Gunn, R.J. / Hollander, J. / Jones, B. / Ketcham, J.M. / Khare, S. / Kuehler, J. / Lawson, J.D. / Marx, M.A. / Olson, P. / Pearson, K.E. / Ren, C. / Tsagris, D. / Ulaganathan, T. / Van't Veer, I. / Wang, X. / Ivetac, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 8t5g.cif.gz | 117.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb8t5g.ent.gz | 87.1 KB | Display | PDB format |
PDBx/mmJSON format | 8t5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/t5/8t5g ftp://data.pdbj.org/pub/pdb/validation_reports/t5/8t5g | HTTPS FTP |
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-Related structure data
Related structure data | 8t5mC 8t5rC 8uc9C 8uf2C 8uh0C 6eieS S: Starting model for refinement C: citing same article (ref.) |
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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: 57370.676 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: SOS2 / Production host: Escherichia coli (E. coli) / References: UniProt: Q07890 | ||||||
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#2: Chemical | ChemComp-DMS / | ||||||
#3: Chemical | ChemComp-SO4 / #4: Chemical | ChemComp-THA / | #5: 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: 2.56 Å3/Da / Density % sol: 52.01 % |
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Crystal grow | Temperature: 281.15 K / Method: vapor diffusion, hanging drop / Details: 10% Peg 3350 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: CLSI / Beamline: 08ID-1 / Wavelength: 1.0332 Å |
Detector | Type: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Mar 21, 2022 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.0332 Å / Relative weight: 1 |
Reflection | Resolution: 1.92→43.9 Å / Num. obs: 40046 / % possible obs: 97 % / Redundancy: 3.6 % / CC1/2: 0.99 / Net I/σ(I): 8.43 |
Reflection shell | Resolution: 1.92→1.97 Å / Num. unique obs: 2819 / CC1/2: 0.27 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 6EIE Resolution: 1.92→43.9 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.942 / SU B: 5.55 / SU ML: 0.147 / Cross valid method: THROUGHOUT / ESU R: 0.17 / ESU R Free: 0.155 / 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: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 39.152 Å2
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Refinement step | Cycle: 1 / Resolution: 1.92→43.9 Å
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Refine LS restraints |
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