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Yorodumi- PDB-6ezx: CATHEPSIN L IN COMPLEX WITH (3S,14E)-19-chloro-N-(1-cyanocyclopro... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ezx | ||||||
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Title | CATHEPSIN L IN COMPLEX WITH (3S,14E)-19-chloro-N-(1-cyanocyclopropyl)-5-oxo-17-oxa-4-azatricyclo[16.2.2.06,11]docosa-1(21),6,8,10,14,18(22),19-heptaene-3-carboxamide | ||||||
Components | Cathepsin L1 | ||||||
Keywords | HYDROLASE / PROTEASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX | ||||||
Function / homology | Function and homology information enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / fibronectin binding / Collagen degradation / antigen processing and presentation / collagen catabolic process / serpin family protein binding / Attachment and Entry / cysteine-type peptidase activity / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / lysosome / symbiont entry into host cell / immune response / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.34 Å | ||||||
Authors | Banner, D.W. / Benz, J. / Kuglstatter, A. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Repurposing a Library of Human Cathepsin L Ligands: Identification of Macrocyclic Lactams as Potent Rhodesain and Trypanosoma brucei Inhibitors. Authors: Giroud, M. / Dietzel, U. / Anselm, L. / Banner, D. / Kuglstatter, A. / Benz, J. / Blanc, J.B. / Gaufreteau, D. / Liu, H. / Lin, X. / Stich, A. / Kuhn, B. / Schuler, F. / Kaiser, M. / Brun, R. ...Authors: Giroud, M. / Dietzel, U. / Anselm, L. / Banner, D. / Kuglstatter, A. / Benz, J. / Blanc, J.B. / Gaufreteau, D. / Liu, H. / Lin, X. / Stich, A. / Kuhn, B. / Schuler, F. / Kaiser, M. / Brun, R. / Schirmeister, T. / Kisker, C. / Diederich, F. / Haap, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ezx.cif.gz | 184.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ezx.ent.gz | 154.6 KB | Display | PDB format |
PDBx/mmJSON format | 6ezx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ez/6ezx ftp://data.pdbj.org/pub/pdb/validation_reports/ez/6ezx | HTTPS FTP |
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-Related 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: 24191.701 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL, CTSL1 / Production host: Escherichia coli (E. coli) / References: UniProt: P07711, cathepsin L #2: Chemical | #3: 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: 2.32 Å3/Da / Density % sol: 46.99 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1 M Bis-Tris |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Apr 1, 2011 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.34→46.39 Å / Num. obs: 15249 / % possible obs: 85.4 % / Redundancy: 3 % / Rmerge(I) obs: 0.07 / Net I/σ(I): 9.5 |
Reflection shell | Resolution: 2.34→2.4 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.599 / Mean I/σ(I) obs: 1.3 / Num. unique obs: 1123 / % possible all: 84.7 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.34→46.39 Å / Cor.coef. Fo:Fc: 0.951 / Cor.coef. Fo:Fc free: 0.904 / SU B: 28.624 / SU ML: 0.321 / Cross valid method: THROUGHOUT / ESU R: 0.883 / ESU R Free: 0.356
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 82.989 Å2
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Refinement step | Cycle: 1 / Resolution: 2.34→46.39 Å
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