+Open data
-Basic information
Entry | Database: PDB / ID: 5qc4 | ||||||||||||
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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 / 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 / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 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: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Thioether acetamides as P3 binding elements for tetrahydropyrido-pyrazole cathepsin S inhibitors. Authors: Wiener, D.K. / Lee-Dutra, A. / Bembenek, S. / Nguyen, S. / Thurmond, R.L. / Sun, S. / Karlsson, L. / Grice, C.A. / Jones, T.K. / Edwards, J.P. | ||||||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5qc4.cif.gz | 107 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5qc4.ent.gz | 86.5 KB | Display | PDB format |
PDBx/mmJSON format | 5qc4.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qc/5qc4 ftp://data.pdbj.org/pub/pdb/validation_reports/qc/5qc4 | 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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2 |
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Unit cell |
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-Components
#1: Protein | Mass: 24516.471 Da / Num. of mol.: 2 / 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 | #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: 2.07 Å3/Da / Density % sol: 40.54 % |
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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: 2.1→48 Å / Num. obs: 23183 / % possible obs: 94.2 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.068 / Net I/σ(I): 16 |
Reflection shell | Resolution: 2.1→2.25 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.195 / Mean I/σ(I) obs: 5.1 / % possible all: 84.6 |
-Phasing
Phasing | Method: molecular replacement |
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→42.1 Å / SU ML: 0.23 / Cross valid method: THROUGHOUT / σ(F): 2.22 / Phase error: 22.73 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→42.1 Å
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Refine LS restraints |
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LS refinement shell |
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