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Open data
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Basic information
Entry | Database: PDB / ID: 1nb5 | |||||||||
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Title | Crystal structure of stefin A in complex with cathepsin H | |||||||||
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![]() | HYDROLASE/HYDROLASE INHIBITOR / CYSTEINE PROTEINASE / AMINOPEPTIDASE / CYSTATIN / ENZYME-INHIBITOR COMPLEX / HYDROLASE-HYDROLASE INHIBITOR complex | |||||||||
Function / homology | ![]() cathepsin H / immune response-regulating signaling pathway / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / positive regulation of peptidase activity / Surfactant metabolism / alveolar lamellar body / negative regulation of peptidase activity / peptidase inhibitor complex ...cathepsin H / immune response-regulating signaling pathway / neuropeptide catabolic process / HLA-A specific activating MHC class I receptor activity / dichotomous subdivision of terminal units involved in lung branching / positive regulation of peptidase activity / Surfactant metabolism / alveolar lamellar body / negative regulation of peptidase activity / peptidase inhibitor complex / membrane protein proteolysis / Formation of the cornified envelope / peptide cross-linking / bradykinin catabolic process / cornified envelope / Neutrophil degranulation / metanephros development / surfactant homeostasis / zymogen activation / MHC class II antigen presentation / cysteine-type endopeptidase inhibitor activity / positive regulation of epithelial cell migration / thyroid hormone binding / cysteine-type endopeptidase activator activity involved in apoptotic process / aminopeptidase activity / response to retinoic acid / cysteine-type peptidase activity / keratinocyte differentiation / ERK1 and ERK2 cascade / proteolysis involved in protein catabolic process / negative regulation of proteolysis / positive regulation of apoptotic signaling pathway / protein destabilization / T cell mediated cytotoxicity / cell-cell adhesion / positive regulation of angiogenesis / endopeptidase activity / protease binding / lysosome / positive regulation of cell migration / immune response / cysteine-type endopeptidase activity / serine-type endopeptidase activity / positive regulation of cell population proliferation / positive regulation of gene expression / negative regulation of apoptotic process / proteolysis / extracellular space / nucleoplasm / cytoplasm / cytosol Similarity search - Function | |||||||||
Biological species | ![]() ![]() ![]() | |||||||||
Method | ![]() ![]() ![]() | |||||||||
![]() | Jenko, S. / Dolenc, I. / Guncar, G. / Dobersek, A. / Podobnik, M. / Turk, D. | |||||||||
![]() | ![]() Title: Crystal structure of stefin A in complex with cathepsin H: N-terminal residues of inhibitors can adapt to the active sites of endo- and exopeptidases Authors: Jenko, S. / Dolenc, I. / Guncar, G. / Dobersek, A. / Podobnik, M. / Turk, D. | |||||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 265.4 KB | Display | ![]() |
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PDB format | ![]() | 214.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.6 MB | Display | ![]() |
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Full document | ![]() | 1.7 MB | Display | |
Data in XML | ![]() | 55.9 KB | Display | |
Data in CIF | ![]() | 75 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1nb3C ![]() 1stfS ![]() 8pchS C: citing same article ( S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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1 | ![]()
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2 | ![]()
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3 | ![]()
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4 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 24328.521 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: spleen / Source: (natural) ![]() ![]() #2: Protein/peptide | Mass: 848.878 Da / Num. of mol.: 4 / Source method: isolated from a natural source / Details: spleen / Source: (natural) ![]() ![]() #3: Protein | Mass: 11020.464 Da / Num. of mol.: 4 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #4: Polysaccharide | beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta- ...beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.51 Å3/Da / Density % sol: 50.63 % | ||||||||||||||||||||||||||||||||||||||||||
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 4.2 Details: PEG 4000, ammonium sulphate, sodium acetate, cadmium chloride, pH 4.2, VAPOR DIFFUSION, SITTING DROP, temperature 298K | ||||||||||||||||||||||||||||||||||||||||||
Crystal grow | *PLUS Temperature: 22 ℃ / Method: vapor diffusion | ||||||||||||||||||||||||||||||||||||||||||
Components of the solutions | *PLUS
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-Data collection
Diffraction | Mean temperature: 90 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Dec 10, 2001 / Details: Toroidal mirror |
Radiation | Monochromator: Diamond (111), Ge(220) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.933 Å / Relative weight: 1 |
Reflection | Resolution: 2.4→38.03 Å / Num. obs: 56687 / % possible obs: 98.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 20.9 % / Rsym value: 0.104 |
Reflection shell | Resolution: 2.4→2.53 Å / Redundancy: 5 % / Rmerge(I) obs: 0.104 / Mean I/σ(I) obs: 4.3 / Num. unique all: 6750 / Rsym value: 0.342 / % possible all: 96.8 |
Reflection | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 99 Å / Num. obs: 56687 / % possible obs: 98.4 % / Num. measured all: 1185453 / Rmerge(I) obs: 0.104 |
Reflection shell | *PLUS Highest resolution: 2.4 Å / Lowest resolution: 2.5 Å / % possible obs: 96.8 % / Rmerge(I) obs: 0.342 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: PDB ENTRY 1STF, 8PCH Resolution: 2.4→10 Å / Isotropic thermal model: Isotropic / Cross valid method: R-FREE,KICKED OMIT MAP / σ(F): 2 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 40.3 Å2 | ||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.4→10 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 10 Å / Num. reflection obs: 41462 | ||||||||||||||||||||
Solvent computation | *PLUS | ||||||||||||||||||||
Displacement parameters | *PLUS |