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Yorodumi- PDB-5e8z: TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH 3-... -
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-Basic information
Entry | Database: PDB / ID: 5e8z | ||||||
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Title | TGF-BETA RECEPTOR TYPE 1 KINASE DOMAIN (T204D) IN COMPLEX WITH 3-AMINO-6-[4-(2-HYDROXYETHYL)PHENYL]-N-[4-(MORPHOLIN-4-YL)PYRIDIN-3-YL]PYRAZINE-2-CARBOXAMIDE | ||||||
Components | TGF-beta receptor type-1 | ||||||
Keywords | TRANSFERASE/TRANSFERASE INHIBITOR / ALK5 / KINASE DOMAIN / TRANSFERASE-TRANSFERASE INHIBITOR COMPLEX | ||||||
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 / mesenchymal cell differentiation / transforming growth factor beta receptor activity, type I / activin receptor complex / neuron fate commitment / positive regulation of extracellular matrix assembly / type II transforming growth factor beta receptor binding / TGFBR1 LBD Mutants in Cancer / germ cell migration / receptor protein serine/threonine kinase / angiogenesis involved in coronary vascular morphogenesis / transmembrane receptor protein serine/threonine kinase activity / pharyngeal system development / activin binding / coronary artery morphogenesis / activin receptor signaling pathway / ventricular trabecula myocardium morphogenesis / filopodium assembly / embryonic cranial skeleton morphogenesis / response to cholesterol / transforming growth factor beta binding / I-SMAD binding / collagen fibril organization / negative regulation of chondrocyte differentiation / endothelial cell activation / skeletal system morphogenesis / endothelial cell proliferation / lens development in camera-type eye / positive regulation of filopodium assembly / anterior/posterior pattern specification / artery morphogenesis / ventricular septum morphogenesis / roof of mouth development / SMAD binding / TGF-beta receptor signaling activates SMADs / 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 stress fiber assembly / cellular response to transforming growth factor beta stimulus / positive regulation of endothelial cell proliferation / negative regulation of cell migration / Downregulation of TGF-beta receptor signaling / transforming growth factor beta receptor signaling pathway / post-embryonic development / TGF-beta receptor signaling in EMT (epithelial to mesenchymal transition) / thymus development / kidney development / skeletal system development / cell motility / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of apoptotic signaling pathway / wound healing / cellular response to growth factor stimulus / UCH proteinases / male gonad development / 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 / Ub-specific processing proteases / regulation of cell cycle / protein kinase activity / intracellular signal transduction / endosome / 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 / MOLECULAR REPLACEMENT / Resolution: 1.51 Å | ||||||
Authors | Sheriff, S. | ||||||
Citation | Journal: Acta Crystallogr D Struct Biol / Year: 2016 Title: Crystal structures of apo and inhibitor-bound TGF beta R2 kinase domain: insights into TGF beta R isoform selectivity. Authors: Tebben, A.J. / Ruzanov, M. / Gao, M. / Xie, D. / Kiefer, S.E. / Yan, C. / Newitt, J.A. / Zhang, L. / Kim, K. / Lu, H. / Kopcho, L.M. / Sheriff, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5e8z.cif.gz | 82.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5e8z.ent.gz | 58.8 KB | Display | PDB format |
PDBx/mmJSON format | 5e8z.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5e8z_validation.pdf.gz | 436.9 KB | Display | wwPDB validaton report |
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Full document | 5e8z_full_validation.pdf.gz | 438 KB | Display | |
Data in XML | 5e8z_validation.xml.gz | 14.6 KB | Display | |
Data in CIF | 5e8z_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/e8/5e8z ftp://data.pdbj.org/pub/pdb/validation_reports/e8/5e8z | HTTPS FTP |
-Related structure data
Related structure data | 5e8sC 5e8tC 5e8uC 5e8vC 5e8wC 5e8xC 5e8yC 5e90C 5e91C 5e92C 3tzmS C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35165.473 Da / Num. of mol.: 1 / Fragment: KINASE DOMAIN, UNP RESIDUES 200-503 / Mutation: T204D Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: TGFBR1, ALK5, SKR4 / Plasmid: PFASTBAC1 / Production host: SPODOPTERA FRUGIPERDA (fall armyworm) References: UniProt: P36897, receptor protein serine/threonine kinase |
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#2: Chemical | ChemComp-5L4 / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.99 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5.6 / Details: 23%(w/v) PEG3350, 3%(v/v) glcyerol |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 17-ID / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: May 30, 2014 / Details: KIRKPATRICK-BAEZ |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.51→42.09 Å / Num. obs: 46811 / % possible obs: 99.9 % / Observed criterion σ(I): 0 / Redundancy: 6.5 % / Biso Wilson estimate: 19.53 Å2 / Rsym value: 0.047 / Net I/σ(I): 19.6 |
Reflection shell | Resolution: 1.51→1.69 Å / Redundancy: 6.6 % / Rmerge(I) obs: 0.383 / Mean I/σ(I) obs: 4.2 / Rejects: 0 / % possible all: 99.8 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3TZM Resolution: 1.51→15.22 Å / Cor.coef. Fo:Fc: 0.9582 / Cor.coef. Fo:Fc free: 0.9403 / SU R Cruickshank DPI: 0.074 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.077 / SU Rfree Blow DPI: 0.076 / SU Rfree Cruickshank DPI: 0.074
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Displacement parameters | Biso max: 92.5 Å2 / Biso mean: 23.29 Å2 / Biso min: 9.46 Å2
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Refine analyze | Luzzati coordinate error obs: 0.166 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: final / Resolution: 1.51→15.22 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.51→1.55 Å / Total num. of bins used: 20
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