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Yorodumi- PDB-1ft4: PHOTOCHEMICALLY-ENHANCED BINDING OF SMALL MOLECULES TO THE TUMOR ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 1ft4 | ||||||
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Title | PHOTOCHEMICALLY-ENHANCED BINDING OF SMALL MOLECULES TO THE TUMOR NECROSIS FACTOR RECEPTOR-1 | ||||||
Components | SOLUBLE TUMOR NECROSIS FACTOR RECEPTOR 1 | ||||||
Keywords | SIGNALING PROTEIN / BINDING PROTEIN / CYTOKINE | ||||||
Function / homology | Function and homology information positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding ...positive regulation of amide metabolic process / tumor necrosis factor receptor superfamily complex / pulmonary valve development / aortic valve development / tumor necrosis factor receptor activity / positive regulation of lipid metabolic process / negative regulation of extracellular matrix constituent secretion / regulation of membrane lipid metabolic process / positive regulation of apoptotic process involved in morphogenesis / tumor necrosis factor binding / TNFs bind their physiological receptors / negative regulation of cardiac muscle hypertrophy / TNF signaling / TNFR1-mediated ceramide production / regulation of establishment of endothelial barrier / regulation of tumor necrosis factor-mediated signaling pathway / TNFR1-induced proapoptotic signaling / positive regulation of execution phase of apoptosis / prostaglandin metabolic process / Interleukin-10 signaling / extrinsic apoptotic signaling pathway via death domain receptors / positive regulation of tyrosine phosphorylation of STAT protein / tumor necrosis factor-mediated signaling pathway / TNFR1-induced NF-kappa-B signaling pathway / protein localization to plasma membrane / Regulation of TNFR1 signaling / negative regulation of inflammatory response / positive regulation of inflammatory response / cytokine-mediated signaling pathway / cellular response to mechanical stimulus / intrinsic apoptotic signaling pathway in response to DNA damage / positive regulation of canonical NF-kappaB signal transduction / transcription by RNA polymerase II / receptor complex / defense response to bacterium / inflammatory response / membrane raft / Golgi membrane / cell surface / positive regulation of transcription by RNA polymerase II / extracellular space / extracellular region / membrane / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 2.9 Å | ||||||
Authors | Muckelbauer, J.K. / Chang, C.-H. | ||||||
Citation | Journal: Proc.Natl.Acad.Sci.USA / Year: 2001 Title: Photochemically enhanced binding of small molecules to the tumor necrosis factor receptor-1 inhibits the binding of TNF-alpha. Authors: Carter, P.H. / Scherle, P.A. / Muckelbauer, J.K. / Voss, M.E. / Liu, R.Q. / Thompson, L.A. / Tebben, A.J. / Solomon, K.A. / Lo, Y.C. / Li, Z. / Strzemienski, P. / Yang, G. / Falahatpisheh, N. ...Authors: Carter, P.H. / Scherle, P.A. / Muckelbauer, J.K. / Voss, M.E. / Liu, R.Q. / Thompson, L.A. / Tebben, A.J. / Solomon, K.A. / Lo, Y.C. / Li, Z. / Strzemienski, P. / Yang, G. / Falahatpisheh, N. / Xu, M. / Wu, Z. / Farrow, N.A. / Ramnarayan, K. / Wang, J. / Rideout, D. / Yalamoori, V. / Domaille, P. / Underwood, D.J. / Trzaskos, J.M. / Friedman, S.M. / Newton, R.C. / Decicco, C.P. / Muckelbauer, J.A. #1: Journal: J.Biol.Chem. / Year: 1995 Title: Crystallographic Evidence for Dimerization of Unliganded Tumor Necrosis Factor Receptor Authors: Naismith, J.H. / Devine, T.Q. / Brandhuber, B.J. / Sprang, S.R. #2: Journal: Cell(Cambridge,Mass.) / Year: 1993 Title: Crystal Structure of the Soluble Human 55 Kd Tnf Receptor-Human Tnfb Complex: Implication for Tnf Receptor Activation Authors: Banner, D.W. / D'Arcy, A. / Janes, W. / Gentz, W. / Schoenfeld, H.-J. / Broger, C. / Loetscher, H. / Lesslauer, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1ft4.cif.gz | 65.1 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1ft4.ent.gz | 53 KB | Display | PDB format |
PDBx/mmJSON format | 1ft4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ft/1ft4 ftp://data.pdbj.org/pub/pdb/validation_reports/ft/1ft4 | HTTPS FTP |
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-Related structure data
Related structure data | |
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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: 18335.830 Da / Num. of mol.: 2 Fragment: 55 KD EXTRACELLULAR DOMAIN (MET PLUS RESIDUES 12-272) Source method: isolated from a genetically manipulated source Details: N OF ALA 62, CHAIN A IS BOUND TO LIGAND 705 / Source: (gene. exp.) Homo sapiens (human) / Production host: Escherichia coli (E. coli) / References: UniProt: P19438 #2: Chemical | ChemComp-703 / | |
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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: 2.98 Å3/Da / Density % sol: 58.67 % | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 297 K / Method: vapor diffusion, sitting drop / pH: 8.5 Details: MPD, Ammonium Acetate Tris Buffer, pH 8.5, VAPOR DIFFUSION, SITTING DROP at 297K | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 293 K / Details: Rodseth, L.E., (1994) J.Mol.Biol., 239, 332. | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 5ID-B / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Feb 13, 2000 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.9→35 Å / Num. obs: 9191 / % possible obs: 88 % / Rmerge(I) obs: 0.093 / Net I/σ(I): 17 |
-Processing
Software |
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Refinement | Resolution: 2.9→10 Å / σ(F): 2 /
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Refinement step | Cycle: LAST / Resolution: 2.9→10 Å
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Refine LS restraints |
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Software | *PLUS Name: X-PLOR / Version: 3.851 / Classification: refinement | |||||||||||||||
Refinement | *PLUS Lowest resolution: 10 Å / σ(F): 2 / Rfactor obs: 0.274 | |||||||||||||||
Solvent computation | *PLUS | |||||||||||||||
Displacement parameters | *PLUS | |||||||||||||||
Refine LS restraints | *PLUS Type: x_angle_deg / Dev ideal: 3.1 |