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Yorodumi- PDB-3faa: Crystal structure of TGFbRI complexed with a 2-aminoimidazole inh... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3faa | ||||||
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Title | Crystal structure of TGFbRI complexed with a 2-aminoimidazole inhibitor | ||||||
Components | TGF-beta receptor type-1 | ||||||
Keywords | TRANSFERASE / Kinase / TGFbeta / structure-based drug design / protein-inhibitor complex / ATP-binding / Craniosynostosis / Disease mutation / Glycoprotein / Magnesium / Manganese / Membrane / Metal-binding / Nucleotide-binding / Phosphoprotein / Polymorphism / Receptor / Serine/threonine-protein kinase / Transmembrane | ||||||
Function / homology | Function and homology information extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity ...extracellular structure organization / epicardium morphogenesis / parathyroid gland development / transforming growth factor beta ligand-receptor complex / regulation of cardiac muscle cell proliferation / myofibroblast differentiation / positive regulation of tight junction disassembly / positive regulation of epithelial to mesenchymal transition involved in endocardial cushion formation / TGFBR2 Kinase Domain Mutants in Cancer / transforming growth factor beta receptor activity / positive regulation of mesenchymal stem cell proliferation / ventricular compact myocardium morphogenesis / SMAD2/3 Phosphorylation Motif Mutants in Cancer / TGFBR1 KD Mutants in Cancer / positive regulation of vasculature development / regulation of epithelial to mesenchymal transition / activin receptor activity, type I / cardiac epithelial to mesenchymal transition / transforming growth factor beta receptor activity, type I / activin receptor complex / mesenchymal cell differentiation / neuron fate commitment / germ cell migration / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / angiogenesis involved in coronary vascular morphogenesis / receptor protein serine/threonine kinase / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / filopodium assembly / ventricular trabecula myocardium morphogenesis / transforming growth factor beta binding / embryonic cranial skeleton morphogenesis / response to cholesterol / I-SMAD binding / negative regulation of chondrocyte differentiation / collagen fibril organization / endothelial cell proliferation / endothelial cell activation / skeletal system morphogenesis / lens development in camera-type eye / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / TGF-beta receptor signaling activates SMADs / SMAD binding / negative regulation of endothelial cell proliferation / positive regulation of SMAD protein signal transduction / blastocyst development / regulation of protein ubiquitination / endothelial cell migration / bicellular tight junction / epithelial to mesenchymal transition / positive regulation of epithelial to mesenchymal transition / positive regulation of apoptotic signaling pathway / positive regulation of stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / Downregulation of TGF-beta receptor signaling / post-embryonic development / transforming growth factor beta receptor signaling pathway / negative regulation of cell migration / thymus development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / kidney development / skeletal system development / cell motility / negative regulation of extrinsic apoptotic signaling pathway / wound healing / cellular response to growth factor stimulus / male gonad development / UCH proteinases / nervous system development / heart development / positive regulation of cell growth / regulation of gene expression / peptidyl-serine phosphorylation / in utero embryonic development / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / regulation of cell cycle / Ub-specific processing proteases / endosome / protein kinase activity / intracellular signal transduction / positive regulation of cell migration / membrane raft / protein serine/threonine kinase activity / apoptotic process / ubiquitin protein ligase binding / positive regulation of cell population proliferation / positive regulation of gene expression / regulation of DNA-templated transcription / positive regulation of DNA-templated transcription Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 3.35 Å | ||||||
Authors | Boriack-Sjodin, P.A. / Fitch, C. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: 2-Aminoimidazoles inhibitors of TGF-beta receptor 1. Authors: Bonafoux, D. / Chuaqui, C. / Boriack-Sjodin, P.A. / Fitch, C. / Hankins, G. / Josiah, S. / Black, C. / Hetu, G. / Ling, L. / Lee, W.C. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3faa.cif.gz | 329.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3faa.ent.gz | 271.3 KB | Display | PDB format |
PDBx/mmJSON format | 3faa.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fa/3faa ftp://data.pdbj.org/pub/pdb/validation_reports/fa/3faa | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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5 |
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Unit cell |
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-Components
#1: Protein | Mass: 38920.641 Da / Num. of mol.: 5 / Fragment: GS and Kinase domains: UNP residues 162-503 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line: SF9 / Gene: TGFBR1 / Production host: Spodoptera frugiperda (fall armyworm) References: UniProt: P36897, receptor protein serine/threonine kinase #2: Chemical | ChemComp-55F / #3: Chemical | ChemComp-PO4 / |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 3.87 Å3/Da / Density % sol: 68.26 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.4 Details: Na/K phosphate, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 1.1 Å |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Sep 12, 2005 |
Radiation | Monochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.1 Å / Relative weight: 1 |
Reflection | Resolution: 3.2→50 Å / Num. all: 51040 / Num. obs: 50127 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Rmerge(I) obs: 0.127 / Χ2: 1.056 / Net I/σ(I): 13.38 |
Reflection shell | Resolution: 3.2→3.31 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.755 / Num. unique all: 5043 / Χ2: 0.657 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS / Resolution: 3.35→35 Å / Occupancy max: 1 / Occupancy min: 0.5 / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso max: 144.59 Å2 / Biso mean: 71.11 Å2 / Biso min: 7.15 Å2
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Refinement step | Cycle: LAST / Resolution: 3.35→35 Å
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Refine LS restraints |
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Xplor file |
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