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Yorodumi- PDB-3kme: Crystal structure of catalytic domain of TACE with phenyl-pyrroli... -
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-Basic information
Entry | Database: PDB / ID: 3kme | ||||||
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Title | Crystal structure of catalytic domain of TACE with phenyl-pyrrolidinyl-tartrate 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 / positive regulation of leukocyte chemotaxis / 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 / negative regulation of cold-induced thermogenesis / Notch binding / CD163 mediating an anti-inflammatory response / positive regulation of vascular endothelial cell proliferation / cell adhesion mediated by integrin / positive regulation of epidermal growth factor receptor signaling pathway / 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 / integrin binding / actin cytoskeleton / peptidase activity / T cell differentiation in thymus / positive regulation of cell growth / endopeptidase activity / response to lipopolysaccharide / response to hypoxia / cell adhesion / 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 / MOLECULAR REPLACEMENT / Resolution: 1.85 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 | 3kme.cif.gz | 121.3 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3kme.ent.gz | 91.2 KB | Display | PDB format |
PDBx/mmJSON format | 3kme.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3kme_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 3kme_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 3kme_validation.xml.gz | 24.6 KB | Display | |
Data in CIF | 3kme_validation.cif.gz | 34.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/km/3kme ftp://data.pdbj.org/pub/pdb/validation_reports/km/3kme | HTTPS FTP |
-Related structure data
Related structure data | 3kmcC 1bkcS 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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2 |
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Unit cell |
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-Components
-Protein , 1 types, 2 molecules AB
#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 |
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-Non-polymers , 5 types, 304 molecules
#2: Chemical | #3: Chemical | ChemComp-INN / | #4: Chemical | ChemComp-IPA / | #5: Chemical | ChemComp-Z59 / ( | #6: 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: 2.33 Å3/Da / Density % sol: 47.28 % |
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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: ROTATING ANODE / Type: RIGAKU FR-E DW / Wavelength: 1.54178 Å |
Detector | Type: RIGAKU RAXIS IV++ / Detector: IMAGE PLATE / Date: Aug 3, 2006 |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 1.85→50 Å / Num. obs: 49397 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 33.64 Å2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1BKC Resolution: 1.85→27.09 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 36.8 Å2
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Refine analyze | Luzzati coordinate error obs: 0.234 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.85→27.09 Å
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Refine LS restraints |
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