+Open data
-Basic information
Entry | Database: PDB / ID: 2fud | ||||||
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Title | Human Cathepsin S with Inhibitor CRA-27566 | ||||||
Components | cathepsin S | ||||||
Keywords | HYDROLASE / cysteine protease / proteinase / papain / 27566 | ||||||
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 / Resolution: 1.95 Å | ||||||
Authors | Somoza, J.R. | ||||||
Citation | Journal: To be Published Title: Human Cathepsin S with Inhibitor CRA-27566 Authors: Somoza, J.R. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2fud.cif.gz | 99 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2fud.ent.gz | 80.3 KB | Display | PDB format |
PDBx/mmJSON format | 2fud.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/fu/2fud ftp://data.pdbj.org/pub/pdb/validation_reports/fu/2fud | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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1 |
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2 |
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Unit cell |
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Details | The biological unit is probably the monomer, or one half of the asymmetric unit. |
-Components
#1: Protein | Mass: 25006.027 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / 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: 2.77 Å3/Da / Density % sol: 55.61 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion / pH: 5 Details: 22.5%-30% PEG 8K, 0.1 M sodium citrate (pH 5.0), 0.2 M ammonium sulfate, VAPOR DIFFUSION, temperature 293.0K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS IV / Detector: IMAGE PLATE |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 1.73→38.82 Å / Num. obs: 51744 / % possible obs: 87.1 % / Redundancy: 7.78 % / Χ2: 1.12 / Net I/σ(I): 5.3 / Scaling rejects: 3046 |
Reflection shell | Resolution: 1.73→1.79 Å / % possible all: 29.8 |
-Phasing
Phasing MR | Rfactor: 0.494 / Cor.coef. Fo:Fc: 0.39
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-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.95→38.82 Å / FOM work R set: 0.895 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 17.913 Å2
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Refinement step | Cycle: LAST / Resolution: 1.95→38.82 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 50
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Xplor file |
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