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Yorodumi- PDB-2hh5: Crystal Structure of Cathepsin S in complex with a Zinc mediated ... -
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-Basic information
Entry | Database: PDB / ID: 2hh5 | ||||||
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Title | Crystal Structure of Cathepsin S in complex with a Zinc mediated non-covalent arylaminoethyl amide | ||||||
Components | Cathepsin S | ||||||
Keywords | HYDROLASE / Cathepsin S / noncovalent / inhibition / zinc / arylaminoethyl-amides | ||||||
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 / positive regulation of apoptotic signaling pathway / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / proteolysis involved in protein catabolic process / lysosomal lumen / 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 / ficolin-1-rich granule lumen / adaptive immune response / 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: 1.8 Å | ||||||
Authors | Spraggon, G. / Hornsby, M. / Lesley, S.A. / Tully, D.C. / Harris, J.L. / Karenewsky, D.S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Synthesis and SAR of arylaminoethyl amides as noncovalent inhibitors of cathepsin S: P3 cyclic ethers. Authors: Tully, D.C. / Liu, H. / Chatterjee, A.K. / Alper, P.B. / Epple, R. / Williams, J.A. / Roberts, M.J. / Woodmansee, D.H. / Masick, B.T. / Tumanut, C. / Li, J. / Spraggon, G. / Hornsby, M. / ...Authors: Tully, D.C. / Liu, H. / Chatterjee, A.K. / Alper, P.B. / Epple, R. / Williams, J.A. / Roberts, M.J. / Woodmansee, D.H. / Masick, B.T. / Tumanut, C. / Li, J. / Spraggon, G. / Hornsby, M. / Chang, J. / Tuntland, T. / Hollenbeck, T. / Gordon, P. / Harris, J.L. / Karanewsky, D.S. #1: Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Synthesis and evaluation of arylaminoethyl amides as noncovalent inhibitors of cathepsin S. Part 3: heterocyclic P3. Authors: Tully, D.C. / Liu, H. / Alper, P.B. / Chatterjee, A.K. / Epple, R. / Roberts, M.J. / Williams, J.A. / Nguyen, K.T. / Woodmansee, D.H. / Tumanut, C. / Li, J. / Spraggon, G. / Chang, J. / ...Authors: Tully, D.C. / Liu, H. / Alper, P.B. / Chatterjee, A.K. / Epple, R. / Roberts, M.J. / Williams, J.A. / Nguyen, K.T. / Woodmansee, D.H. / Tumanut, C. / Li, J. / Spraggon, G. / Chang, J. / Tuntland, T. / Harris, J.L. / Karanewsky, D.S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2hh5.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2hh5.ent.gz | 81.9 KB | Display | PDB format |
PDBx/mmJSON format | 2hh5.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hh/2hh5 ftp://data.pdbj.org/pub/pdb/validation_reports/hh/2hh5 | HTTPS FTP |
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-Related structure data
Related structure data | 2hhnC 2f1gS S: Starting model for refinement C: citing same article (ref.) |
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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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Details | The biological assembly is a monomer - there are two monomers in the asymmetric unit. |
-Components
#1: Protein | Mass: 24391.393 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P25774, cathepsin S #2: Chemical | ChemComp-ZN / #3: Chemical | #4: Chemical | #5: 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: 2.33 Å3/Da / Density % sol: 47.24 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.2M ZnAcetate, 20% PEG-3350, 150mM Sodium Chloride, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 277K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 5.0.3 / Wavelength: 1 Å |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Sep 28, 2003 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→34.2 Å / Num. all: 38549 / Num. obs: 38549 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2.7 % / Rmerge(I) obs: 0.064 / Rsym value: 0.064 / Net I/σ(I): 17.7 |
Reflection shell | Resolution: 1.8→1.86 Å / Redundancy: 2.5 % / Rmerge(I) obs: 0.763 / Mean I/σ(I) obs: 1.3 / Num. unique all: 4514 / Rsym value: 0.763 / % possible all: 98.2 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2F1G Resolution: 1.8→34.2 Å / Cor.coef. Fo:Fc: 0.97 / Cor.coef. Fo:Fc free: 0.951 / SU B: 3.355 / SU ML: 0.101 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.127 / ESU R Free: 0.126 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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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: 27.905 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→34.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.8→1.847 Å / Total num. of bins used: 20
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