+Open data
-Basic information
Entry | Database: PDB / ID: 2r9m | ||||||
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Title | Cathepsin S complexed with Compound 15 | ||||||
Components | Cathepsin S | ||||||
Keywords | HYDROLASE / CATHEPSIN / PROTEASE / Glycoprotein / Lysosome / Polymorphism / Thiol protease / Zymogen | ||||||
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 / antigen processing and presentation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / laminin binding / phagocytic vesicle / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / positive regulation of apoptotic signaling pathway / proteolysis involved in protein catabolic process / 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 / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / Resolution: 1.97 Å | ||||||
Authors | Ward, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. ...Ward, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. / Hrapchak, M. / DeTuri, M. / White, A. / Crane, K.M. / White, D.M. / Wang, Y. / Hao, M.-H. / Grygon, C.A. / Labadia, M.E. / Wildeson, J. / Freeman, D. / Nelson, R. / Capolino, A. / Peterson, J.D. / Raymond, E.L. / Brown, M.L. / Spero, D.M. | ||||||
Citation | Journal: To be Published Title: Design and Synthesis of Reversible Inhibitors of Cathepsin S: alpha,alpha-Disubstitution at the P1 Residue Provides Potent Inhibitors in Cellular Assays and In Vivo Models of Antigen Presentation Authors: Ward, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. / Hrapchak, M. / DeTuri, M. / White, A. / Crane, K. ...Authors: Ward, Y.D. / Emmanuel, M.J. / Thomson, D.S. / Liu, W. / Bekkali, Y. / Frye, L.L. / Girardot, M. / Morwick, T. / Young, E.R.R. / Zindell, R. / Hrapchak, M. / DeTuri, M. / White, A. / Crane, K.M. / White, D.M. / Wang, Y. / Hao, M.-H. / Grygon, C.A. / Labadia, M.E. / Wildeson, J. / Freeman, D. / Nelson, R. / Capolino, A. / Peterson, J.D. / Raymond, E.L. / Brown, M.L. / Spero, D.M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2r9m.cif.gz | 105.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2r9m.ent.gz | 81.4 KB | Display | PDB format |
PDBx/mmJSON format | 2r9m.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/r9/2r9m ftp://data.pdbj.org/pub/pdb/validation_reports/r9/2r9m | HTTPS FTP |
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-Related structure data
Related structure data | 2r9nC 2r9oC 1ms6S 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 on special symmetry positions |
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-Components
#1: Protein | Mass: 24697.670 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Escherichia coli (E. coli) / References: UniProt: P25774, cathepsin S #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: 2.77 Å3/Da / Density % sol: 55.54 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4.6 Details: 100mM NaOAc, 18-35% PEG MME (500-8000), 2 M (NH4)2SO4 with or without 15% glycerol, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418 |
Detector | Type: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Details: Osmic focussing mirrors |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 1.97→50 Å / Num. obs: 38822 / % possible obs: 97 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 14.7 % / Rsym value: 0.161 |
-Processing
Software |
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Refinement | Starting model: pdb entry 1MS6 Resolution: 1.97→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 13.721 Å2 | ||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.97→50 Å
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Refine LS restraints |
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