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- PDB-5j18: Solution structure of Ras Binding Domain (RBD) of B-Raf complexed... -
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Open data
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Basic information
Entry | Database: PDB / ID: 5j18 | ||||||
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Title | Solution structure of Ras Binding Domain (RBD) of B-Raf complexed with Rigosertib (Complex I) | ||||||
![]() | Serine/threonine-protein kinase B-raf | ||||||
![]() | PROTEIN BINDING / MAPK / PI3K | ||||||
Function / homology | ![]() CD4-positive, alpha-beta T cell differentiation / trehalose metabolism in response to stress / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling ...CD4-positive, alpha-beta T cell differentiation / trehalose metabolism in response to stress / CD4-positive or CD8-positive, alpha-beta T cell lineage commitment / negative regulation of synaptic vesicle exocytosis / Signalling to p38 via RIT and RIN / head morphogenesis / myeloid progenitor cell differentiation / ARMS-mediated activation / SHOC2 M1731 mutant abolishes MRAS complex function / Gain-of-function MRAS complexes activate RAF signaling / endothelial cell apoptotic process / negative regulation of fibroblast migration / positive regulation of glucose transmembrane transport / establishment of protein localization to membrane / mitogen-activated protein kinase kinase binding / regulation of T cell differentiation / Negative feedback regulation of MAPK pathway / positive regulation of axonogenesis / Frs2-mediated activation / stress fiber assembly / positive regulation of axon regeneration / face development / synaptic vesicle exocytosis / somatic stem cell population maintenance / MAP kinase kinase activity / thyroid gland development / MAP kinase kinase kinase activity / negative regulation of endothelial cell apoptotic process / positive regulation of substrate adhesion-dependent cell spreading / positive regulation of stress fiber assembly / response to cAMP / cellular response to calcium ion / ERK1 and ERK2 cascade / substrate adhesion-dependent cell spreading / cellular response to nerve growth factor stimulus / thymus development / long-term synaptic potentiation / animal organ morphogenesis / RAF activation / Spry regulation of FGF signaling / Signaling by high-kinase activity BRAF mutants / MAP2K and MAPK activation / visual learning / epidermal growth factor receptor signaling pathway / response to peptide hormone / Negative regulation of MAPK pathway / Signaling by RAF1 mutants / Signaling by moderate kinase activity BRAF mutants / Paradoxical activation of RAF signaling by kinase inactive BRAF / Signaling downstream of RAS mutants / MAPK cascade / Signaling by BRAF and RAF1 fusions / cellular response to xenobiotic stimulus / presynapse / positive regulation of peptidyl-serine phosphorylation / T cell receptor signaling pathway / regulation of cell population proliferation / cell body / T cell differentiation in thymus / scaffold protein binding / negative regulation of neuron apoptotic process / Ras protein signal transduction / positive regulation of ERK1 and ERK2 cascade / non-specific serine/threonine protein kinase / protein kinase activity / neuron projection / protein phosphorylation / intracellular membrane-bounded organelle / protein serine kinase activity / protein serine/threonine kinase activity / calcium ion binding / protein-containing complex binding / positive regulation of gene expression / negative regulation of apoptotic process / mitochondrion / ATP binding / identical protein binding / nucleus / plasma membrane / cytosol Similarity search - Function | ||||||
Biological species | ![]() | ||||||
Method | SOLUTION NMR / DGSA-distance geometry simulated annealing | ||||||
![]() | Dutta, K. / Vasquez-Del Carpio, R. / Aggarwal, A.K. / Reddy, E.P. | ||||||
![]() | ![]() Title: A Small Molecule RAS-Mimetic Disrupts RAS Association with Effector Proteins to Block Signaling. Authors: Athuluri-Divakar, S.K. / Vasquez-Del Carpio, R. / Dutta, K. / Baker, S.J. / Cosenza, S.C. / Basu, I. / Gupta, Y.K. / Reddy, M.V. / Ueno, L. / Hart, J.R. / Vogt, P.K. / Mulholland, D. / Guha, ...Authors: Athuluri-Divakar, S.K. / Vasquez-Del Carpio, R. / Dutta, K. / Baker, S.J. / Cosenza, S.C. / Basu, I. / Gupta, Y.K. / Reddy, M.V. / Ueno, L. / Hart, J.R. / Vogt, P.K. / Mulholland, D. / Guha, C. / Aggarwal, A.K. / Reddy, E.P. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 303.9 KB | Display | ![]() |
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PDB format | ![]() | 254.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
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-Validation report
Summary document | ![]() | 494.3 KB | Display | ![]() |
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Full document | ![]() | 559.9 KB | Display | |
Data in XML | ![]() | 20.6 KB | Display | |
Data in CIF | ![]() | 31.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
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Links
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Assembly
Deposited unit | ![]()
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NMR ensembles |
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Components
#1: Protein | Mass: 10311.078 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() References: UniProt: P15056, non-specific serine/threonine protein kinase |
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#2: Chemical | ChemComp-6FS / |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||
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NMR experiment |
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Sample preparation
Details | Type: solution Contents: 200 uM [U-99% 13C; U-99% 15N] B-RAF-RBD:Rigosertib Complex I, 90% H2O/10% D2O Details: (20 mM KH2PO4, 200 mM NaCl, pH 7.4), 200uM RBD + 1mM Rigosertib (1:5) Label: 15N 13C Sample / Solvent system: 90% H2O/10% D2O |
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Sample | Conc.: 200 uM / Component: B-RAF-RBD:Rigosertib Complex I / Isotopic labeling: [U-99% 13C; U-99% 15N] |
Sample conditions | Details: (20 mM KH2PO4, 200 mM NaCl, pH 7.4) / Ionic strength: 200 mM / Label: condition1 / pH: 7.4 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer |
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Processing
NMR software |
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Refinement | Method: DGSA-distance geometry simulated annealing / Software ordinal: 1 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the least restraint violations Conformers calculated total number: 1024 / Conformers submitted total number: 10 |