+Open data
-Basic information
Entry | Database: PDB / ID: 5qch | |||||||||
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Title | Crystal structure of human Cathepsin-S with bound ligand | |||||||||
Components | Cathepsin S | |||||||||
Keywords | HYDROLASE / D3R / Cathepsin S / Ligand Docking | |||||||||
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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.2 Å | |||||||||
Model details | Structures re-refined for D3R docking challenge | |||||||||
Authors | Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K. | |||||||||
Citation | Journal: To be published Title: Crystal structure of human Cathepsin-S with bound ligand Authors: Bembenek, S.D. / Ameriks, M.K. / Mirzadegan, T. / Yang, H. / Shao, C. / Burley, S.K. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qch.cif.gz | 369 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qch.ent.gz | 315 KB | Display | PDB format |
PDBx/mmJSON format | 5qch.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/5qch ftp://data.pdbj.org/pub/pdb/validation_reports/qc/5qch | HTTPS FTP |
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-Group deposition
ID | G_1002040 (26 entries) |
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Title | Ligand binding to Cathepsin S |
Type | undefined |
Description | Ligand binding to Cathepsin S |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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Unit cell |
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-Components
#1: Protein | Mass: 24516.471 Da / Num. of mol.: 4 / Mutation: C139S 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-SO4 / #3: Chemical | ChemComp-BJS / #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: 2.84 Å3/Da / Density % sol: 56.76 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5 Details: 100MM SODIUM ACETATE PH 4.5, 200MM AMMONIUM ACETATE, 25% PEG 8000. PROTEIN CONCENTRATION 7 MG/ML, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54178 |
Detector | Type: RIGAKU SATURN 944 / Detector: CCD / Date: May 10, 2006 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54178 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→34.11 Å / Num. obs: 51559 / % possible obs: 94.2 % |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.2→34.11 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.932 / SU R Cruickshank DPI: 0.296 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.351 / SU Rfree Blow DPI: 0.234 / SU Rfree Cruickshank DPI: 0.224
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Displacement parameters | Biso mean: 19.32 Å2
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Refine analyze | Luzzati coordinate error obs: 0.3 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→34.11 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.2→2.26 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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