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Yorodumi- PDB-4p6g: Crystal Structure of Human Cathepsin S Bound to a Non-covalent In... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4p6g | ||||||
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Title | Crystal Structure of Human Cathepsin S Bound to a Non-covalent Inhibitor. | ||||||
Components | Cathepsin S | ||||||
Keywords | HYDROLASE/HYDROLASE INHIBITOR / cathespsin S / non-covalent inhibitor / cysteine protease / HYDROLASE-HYDROLASE INHIBITOR complex | ||||||
Function / homology | Function and homology information cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / antigen processing and presentation / collagen catabolic process / extracellular matrix disassembly / laminin binding / phagocytic vesicle / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / Endosomal/Vacuolar pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / Neutrophil degranulation / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å | ||||||
Authors | Wang, Y. / Jadhav, P.K. | ||||||
Citation | Journal: Acs Med.Chem.Lett. / Year: 2014 Title: Discovery of Cathepsin S Inhibitor LY3000328 for the Treatment of Abdominal Aortic Aneurysm. Authors: Jadhav, P.K. / Schiffler, M.A. / Gavardinas, K. / Kim, E.J. / Matthews, D.P. / Staszak, M.A. / Coffey, D.S. / Shaw, B.W. / Cassidy, K.C. / Brier, R.A. / Zhang, Y. / Christie, R.M. / Matter, ...Authors: Jadhav, P.K. / Schiffler, M.A. / Gavardinas, K. / Kim, E.J. / Matthews, D.P. / Staszak, M.A. / Coffey, D.S. / Shaw, B.W. / Cassidy, K.C. / Brier, R.A. / Zhang, Y. / Christie, R.M. / Matter, W.F. / Qing, K. / Durbin, J.D. / Wang, Y. / Deng, G.G. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4p6g.cif.gz | 201.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4p6g.ent.gz | 161.3 KB | Display | PDB format |
PDBx/mmJSON format | 4p6g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p6/4p6g ftp://data.pdbj.org/pub/pdb/validation_reports/p6/4p6g | HTTPS FTP |
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-Related structure data
-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 25135.141 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Enterobacteria phage L1 (virus) / References: UniProt: P25774, cathepsin S #2: Chemical | ChemComp-2FZ / ( #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: 2.59 Å3/Da / Density % sol: 52.56 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 4.6 / Details: PEG 8000, ammonium sulfate, sodium acetate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Jul 10, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.979 Å / Relative weight: 1 |
Reflection | Resolution: 1.58→65.21 Å / Num. obs: 138388 / % possible obs: 94.5 % / Redundancy: 2 % / Net I/σ(I): 2.1 |
-Processing
Software | Name: REFMAC / Version: 5.6.0050 / Classification: refinement | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.58→65.21 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.946 / SU B: 1.642 / SU ML: 0.059 / Cross valid method: THROUGHOUT / ESU R: 0.09 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD
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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: 19.84 Å2
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Refinement step | Cycle: 1 / Resolution: 1.58→65.21 Å
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