+Open data
-Basic information
Entry | Database: PDB / ID: 4bsq | ||||||
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Title | MOUSE CATHEPSIN S WITH COVALENT LIGAND | ||||||
Components | CATHEPSIN S | ||||||
Keywords | HYDROLASE / CYSTEINE PROTEASE | ||||||
Function / homology | Function and homology information Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cathepsin S / Degradation of the extracellular matrix / basement membrane disassembly / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / cysteine-type peptidase activity ...Trafficking and processing of endosomal TLR / Assembly of collagen fibrils and other multimeric structures / cathepsin S / Degradation of the extracellular matrix / basement membrane disassembly / positive regulation of cation channel activity / MHC class II antigen presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / bone resorption / cysteine-type peptidase activity / phagocytic vesicle / Neutrophil degranulation / proteolysis involved in protein catabolic process / early endosome lumen / positive regulation of apoptotic signaling pathway / positive regulation of inflammatory response / antigen processing and presentation of exogenous peptide antigen via MHC class II / peptidase activity / lysosome / immune response / cysteine-type endopeptidase activity / cell surface / proteolysis / extracellular space / membrane Similarity search - Function | ||||||
Biological species | MUS MUSCULUS (house mouse) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.96 Å | ||||||
Authors | Banner, D.W. / Benz, J. / Gsell, B. / Stihle, M. / Ruf, A. / Hilpert, H. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2013 Title: Identification of Potent and Selective Cathepsin S (Cats) Inhibitors Containing Different Central Cyclic Scaffolds. Authors: Hilpert, H. / Mauser, H. / Humm, R. / Anselm, L. / Kuehne, H. / Hartmann, G. / Gruener, S. / Banner, D.W. / Benz, J. / Gsell, B. / Kuglstatter, A. / Stihle, M. / Thoma, R. / Alvarez-Sanchez, ...Authors: Hilpert, H. / Mauser, H. / Humm, R. / Anselm, L. / Kuehne, H. / Hartmann, G. / Gruener, S. / Banner, D.W. / Benz, J. / Gsell, B. / Kuglstatter, A. / Stihle, M. / Thoma, R. / Alvarez-Sanchez, R. / Iding, H. / Wirz, B. / Haap, W. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bsq.cif.gz | 60.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bsq.ent.gz | 43.6 KB | Display | PDB format |
PDBx/mmJSON format | 4bsq.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bs/4bsq ftp://data.pdbj.org/pub/pdb/validation_reports/bs/4bsq | 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24662.480 Da / Num. of mol.: 1 / Fragment: CATHEPSIN S, RESIDUES 116-340 Source method: isolated from a genetically manipulated source Source: (gene. exp.) MUS MUSCULUS (house mouse) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O70370, cathepsin S | ||||
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#2: Chemical | ChemComp-QQV / ( | ||||
#3: Chemical | ChemComp-SO4 / #4: Water | ChemComp-HOH / | Sequence details | 116-340 NO MUTATIONS 218 MET IS VARIANT | |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.53 Å3/Da / Density % sol: 51.5 % / Description: NONE |
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Crystal grow | pH: 5.5 / Details: 2M AM2SO4, 0.1M BISTRIS PH 5.5 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 1 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Aug 13, 2007 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.96→49.45 Å / Num. obs: 16810 / % possible obs: 96.1 % / Observed criterion σ(I): -3 / Redundancy: 3.79 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 14.83 |
Reflection shell | Resolution: 1.96→2.08 Å / Redundancy: 3.61 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 4.28 / % possible all: 88 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: IN HOUSE STRUCTURES Resolution: 1.96→18.66 Å / Cor.coef. Fo:Fc: 0.955 / Cor.coef. Fo:Fc free: 0.938 / SU B: 3.921 / SU ML: 0.109 / Cross valid method: THROUGHOUT / ESU R: 0.167 / ESU R Free: 0.148 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. U VALUES REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 22.877 Å2
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Refinement step | Cycle: LAST / Resolution: 1.96→18.66 Å
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