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Yorodumi- PDB-5mqy: CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-pheno... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5mqy | ||||||
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Title | CATHEPSIN L IN COMPLEX WITH 4-[1,3-benzodioxol-5-ylmethyl(2-phenoxyethyl)amino]-5-fluoropyrimidine-2-carbonitrile | ||||||
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 / serpin family protein binding / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen ...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 / serpin family protein binding / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / antigen processing and presentation / fibronectin binding / protein autoprocessing / Collagen degradation / collagen catabolic process / cysteine-type peptidase activity / Attachment and Entry / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / 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 / apical plasma membrane / symbiont entry into host cell / immune response / 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: 1.13 Å | ||||||
Authors | Kuglstatter, A. / Stihle, M. / Benz, J. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2017 Title: Prospective Evaluation of Free Energy Calculations for the Prioritization of Cathepsin L Inhibitors. Authors: Kuhn, B. / Tichy, M. / Wang, L. / Robinson, S. / Martin, R.E. / Kuglstatter, A. / Benz, J. / Giroud, M. / Schirmeister, T. / Abel, R. / Diederich, F. / Hert, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5mqy.cif.gz | 114.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5mqy.ent.gz | 88.6 KB | Display | PDB format |
PDBx/mmJSON format | 5mqy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5mqy_validation.pdf.gz | 790.9 KB | Display | wwPDB validaton report |
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Full document | 5mqy_full_validation.pdf.gz | 795.9 KB | Display | |
Data in XML | 5mqy_validation.xml.gz | 14.7 KB | Display | |
Data in CIF | 5mqy_validation.cif.gz | 21.4 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/mq/5mqy ftp://data.pdbj.org/pub/pdb/validation_reports/mq/5mqy | HTTPS FTP |
-Related structure data
Related structure data | 5f02S 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: 24191.701 Da / Num. of mol.: 1 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 | ||
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#2: Chemical | ChemComp-GH4 / | ||
#3: Chemical | ChemComp-EDO / #4: 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: 2.06 Å3/Da / Density % sol: 40.15 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 25% PEG3350, 0.1M 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: Aug 12, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.13→39.26 Å / Num. obs: 75222 / % possible obs: 99.8 % / Redundancy: 6.15 % / Rmerge(I) obs: 0.0428 / Rsym value: 0.0428 / Net I/σ(I): 13.65 |
Reflection shell | Resolution: 1.13→1.23 Å / Redundancy: 5.75 % / Rmerge(I) obs: 0.785 / Mean I/σ(I) obs: 1.04 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5F02 Resolution: 1.13→39.26 Å / Cor.coef. Fo:Fc: 0.983 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.018 / SU ML: 0.038 / Cross valid method: THROUGHOUT / ESU R: 0.033 / ESU R Free: 0.038
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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: 23.934 Å2
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Refinement step | Cycle: LAST / Resolution: 1.13→39.26 Å
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