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Yorodumi- PDB-3kmc: Crystal structure of catalytic domain of TACE with tartrate-based... -
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-Basic information
Entry | Database: PDB / ID: 3kmc | ||||||
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Title | Crystal structure of catalytic domain of TACE with tartrate-based inhibitor | ||||||
Components | TNF-alpha-converting enzyme | ||||||
Keywords | HYDROLASE / A disintegrin and metalloproteinase domain 17 / TNF-alpha-converting enzyme / TNF-alpha convertase / Snake venom-like protease / Cleavage on pair of basic residues / Glycoprotein / Membrane / Metal-binding / Metalloprotease / Notch signaling pathway / Phosphoprotein / Protease / Zymogen | ||||||
Function / homology | Function and homology information ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding ...ADAM 17 endopeptidase / regulation of mast cell apoptotic process / signal release / metalloendopeptidase activity involved in amyloid precursor protein catabolic process / cellular response to high density lipoprotein particle stimulus / positive regulation of epidermal growth factor-activated receptor activity / Constitutive Signaling by NOTCH1 t(7;9)(NOTCH1:M1580_K2555) Translocation Mutant / Notch receptor processing / interleukin-6 receptor binding / tumor necrosis factor binding / positive regulation of T cell chemotaxis / TNF signaling / germinal center formation / Regulated proteolysis of p75NTR / Release of Hh-Np from the secreting cell / commissural neuron axon guidance / positive regulation of tumor necrosis factor-mediated signaling pathway / neutrophil mediated immunity / wound healing, spreading of epidermal cells / Notch binding / negative regulation of cold-induced thermogenesis / positive regulation of leukocyte chemotaxis / CD163 mediating an anti-inflammatory response / positive regulation of vascular endothelial cell proliferation / positive regulation of epidermal growth factor receptor signaling pathway / cell adhesion mediated by integrin / Signaling by EGFR / cytokine binding / amyloid precursor protein catabolic process / membrane protein ectodomain proteolysis / Collagen degradation / positive regulation of cyclin-dependent protein serine/threonine kinase activity / positive regulation of blood vessel endothelial cell migration / positive regulation of G1/S transition of mitotic cell cycle / Growth hormone receptor signaling / positive regulation of chemokine production / Nuclear signaling by ERBB4 / Notch signaling pathway / spleen development / Constitutive Signaling by NOTCH1 HD Domain Mutants / Activated NOTCH1 Transmits Signal to the Nucleus / B cell differentiation / PDZ domain binding / cell motility / negative regulation of transforming growth factor beta receptor signaling pathway / protein processing / metalloendopeptidase activity / Constitutive Signaling by NOTCH1 PEST Domain Mutants / Constitutive Signaling by NOTCH1 HD+PEST Domain Mutants / SH3 domain binding / metallopeptidase activity / positive regulation of tumor necrosis factor production / actin cytoskeleton / integrin binding / peptidase activity / T cell differentiation in thymus / positive regulation of cell growth / endopeptidase activity / response to lipopolysaccharide / cell adhesion / response to hypoxia / defense response to Gram-positive bacterium / positive regulation of cell migration / response to xenobiotic stimulus / membrane raft / apical plasma membrane / endoplasmic reticulum lumen / Golgi membrane / positive regulation of cell population proliferation / cell surface / proteolysis / membrane / metal ion binding / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å | ||||||
Authors | Orth, P. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: The discovery of novel tartrate-based TNF-alpha converting enzyme (TACE) inhibitors. Authors: Rosner, K.E. / Guo, Z. / Orth, P. / Shipps, G.W. / Belanger, D.B. / Chan, T.Y. / Curran, P.J. / Dai, C. / Deng, Y. / Girijavallabhan, V.M. / Hong, L. / Lavey, B.J. / Lee, J.F. / Li, D. / ...Authors: Rosner, K.E. / Guo, Z. / Orth, P. / Shipps, G.W. / Belanger, D.B. / Chan, T.Y. / Curran, P.J. / Dai, C. / Deng, Y. / Girijavallabhan, V.M. / Hong, L. / Lavey, B.J. / Lee, J.F. / Li, D. / Liu, Z. / Popovici-Muller, J. / Ting, P.C. / Vaccaro, H. / Wang, L. / Wang, T. / Yu, W. / Zhou, G. / Niu, X. / Sun, J. / Kozlowski, J.A. / Lundell, D.J. / Madison, V. / McKittrick, B. / Piwinski, J.J. / Shih, N.Y. / Arshad Siddiqui, M. / Strickland, C.O. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3kmc.cif.gz | 121.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kmc.ent.gz | 91.7 KB | Display | PDB format |
PDBx/mmJSON format | 3kmc.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kmc_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3kmc_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3kmc_validation.xml.gz | 23.7 KB | Display | |
Data in CIF | 3kmc_validation.cif.gz | 34.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/3kmc ftp://data.pdbj.org/pub/pdb/validation_reports/km/3kmc | HTTPS FTP |
-Related structure data
Related structure data | 3kmeC 1bkcS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 30569.135 Da / Num. of mol.: 2 / Fragment: residues 215-476 / Mutation: S266A, V353G, Q452N Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: ADAM17, CSVP, TACE / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P78536, ADAM 17 endopeptidase #2: Chemical | #3: Chemical | ChemComp-INN / | #4: Chemical | ChemComp-403 / ( | #5: Water | ChemComp-HOH / | |
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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: 2.4 Å3/Da / Density % sol: 48.74 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 5.6 Details: 15% PEG 6000, 10% 2-Propanol, 100 mM sodium citrate, pH 5.6, VAPOR DIFFUSION, temperature 295K |
-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: ADSC QUANTUM 210 / Detector: CCD / Date: Aug 3, 2006 Details: Use of the IMCA-CAT beamline 17-ID at the Advanced Photon Source was supported by the companies of the Industrial Macromolecular Crystallography Association through a contract with the ...Details: Use of the IMCA-CAT beamline 17-ID at the Advanced Photon Source was supported by the companies of the Industrial Macromolecular Crystallography Association through a contract with the Center for Advanced Radiation Sources at the University of Chicago. Use of the Advanced Photon Source was supported by the U. S. Department of Energy, Office of Science, Office of Basic Energy Sciences, under Contract No. W-31-109-Eng-38 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. obs: 54154 / % possible obs: 97.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 28.74 Å2 |
Reflection shell | Resolution: 1.8→1.83 Å / % possible all: 5 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1bkc Resolution: 1.8→37.16 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 34.73 Å2
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Refine analyze | Luzzati coordinate error obs: 0.321 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.8→37.16 Å
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Refine LS restraints |
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