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Yorodumi- PDB-2h7j: Crystal Structure of Cathepsin S in complex with a Nonpeptidic In... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2h7j | ||||||
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Title | Crystal Structure of Cathepsin S in complex with a Nonpeptidic Inhibitor. | ||||||
Components | Cathepsin S | ||||||
Keywords | HYDROLASE / CATHEPSIN S / Nonpeptidic / chloromethylketone / substrate activity screening | ||||||
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 / phagocytic vesicle / laminin binding / collagen binding / Degradation of the extracellular matrix / MHC class II antigen presentation / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling 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 / 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å | ||||||
Authors | Patterson, A.W. / Wood, W.J. / Hornsby, M. / Lesley, S. / Spraggon, G. / Ellman, J.A. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2006 Title: Identification of selective, nonpeptidic nitrile inhibitors of cathepsin s using the substrate activity screening method. Authors: Patterson, A.W. / Wood, W.J. / Hornsby, M. / Lesley, S. / Spraggon, G. / Ellman, J.A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2h7j.cif.gz | 110.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2h7j.ent.gz | 84.7 KB | Display | PDB format |
PDBx/mmJSON format | 2h7j.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2h7j_validation.pdf.gz | 1.4 MB | Display | wwPDB validaton report |
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Full document | 2h7j_full_validation.pdf.gz | 1.5 MB | Display | |
Data in XML | 2h7j_validation.xml.gz | 25 KB | Display | |
Data in CIF | 2h7j_validation.cif.gz | 37.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/h7/2h7j ftp://data.pdbj.org/pub/pdb/validation_reports/h7/2h7j | HTTPS FTP |
-Related structure data
Related structure data | 2hxzC 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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2 |
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Unit cell |
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Components on special symmetry positions |
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-Components
#1: Protein | Mass: 24391.393 Da / Num. of mol.: 2 / Fragment: Cathepsin S 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 | #3: Chemical | ChemComp-P15 / | #4: Water | ChemComp-HOH / | Has protein modification | Y | |
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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: 2.8 Å3/Da / Density % sol: 56.14 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, sitting drop / pH: 5 Details: 30% Peg-6000, 0.1M Lithium Chloride in Citrate Buffer pH 5.0, 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 315 / Detector: CCD / Date: Jul 25, 2005 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→38.6 Å / Num. all: 92453 / Num. obs: 92453 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.073 / Rsym value: 0.073 / Net I/σ(I): 27.4 |
Reflection shell | Resolution: 1.5→1.53 Å / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 2.7 / Rsym value: 0.642 / % possible all: 95.3 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 2f1g Resolution: 1.5→38.6 Å / Cor.coef. Fo:Fc: 0.967 / Cor.coef. Fo:Fc free: 0.96 / SU B: 1.034 / SU ML: 0.039 / Cross valid method: THROUGHOUT / ESU R: 0.06 / ESU R Free: 0.06 / 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: 12.293 Å2
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Refinement step | Cycle: LAST / Resolution: 1.5→38.6 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.5→1.539 Å / Total num. of bins used: 20
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