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Open data
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Basic information
Entry | Database: PDB / ID: 3kse | ||||||
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Title | Unreduced cathepsin L in complex with stefin A | ||||||
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![]() | Hydrolase/Hydrolase inhibitor / cathepsin / protease-inhibitor complex / stefin / cystatin / papain-like / cysteine protease / Hydrolase / Lysosome / Protease / Thiol protease / Zymogen / Thiol protease inhibitor / Hydrolase-Hydrolase inhibitor complex | ||||||
Function / homology | ![]() negative regulation of peptidase activity / enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / peptidase inhibitor complex / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / Formation of the cornified envelope ...negative regulation of peptidase activity / enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / peptidase inhibitor complex / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / Formation of the cornified envelope / peptide cross-linking / cornified envelope / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / zymogen activation / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase inhibitor activity / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / protein autoprocessing / Collagen degradation / collagen catabolic process / serpin family protein binding / cysteine-type peptidase activity / keratinocyte differentiation / Attachment and Entry / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / lysosomal lumen / proteolysis involved in protein catabolic process / negative regulation of proteolysis / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / cell-cell adhesion / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / adaptive immune response / protease binding / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / lysosome / symbiont entry into host cell / immune response / apical plasma membrane / fusion of virus membrane with host plasma membrane / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / fusion of virus membrane with host endosome membrane / Golgi apparatus / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / nucleus / plasma membrane / cytoplasm / cytosol Similarity search - Function | ||||||
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Method | ![]() ![]() ![]() | ||||||
![]() | Renko, M. / Turk, D. | ||||||
![]() | ![]() Title: Unreduced cathepsin L in complex with stefin A Authors: Renko, 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 | ![]() | 220.8 KB | Display | ![]() |
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PDB format | ![]() | 174.7 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 469.4 KB | Display | ![]() |
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Full document | ![]() | 483.1 KB | Display | |
Data in XML | ![]() | 49 KB | Display | |
Data in CIF | ![]() | 73.2 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1icfS ![]() 3kfqS ![]() 3a9n 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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Unit cell |
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Components
#1: Protein | Mass: 24208.754 Da / Num. of mol.: 3 / Mutation: T110A,N179D Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Protein | Mass: 11020.464 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() ![]() #3: Water | ChemComp-HOH / | Sequence details | CATHEPSIN L WAS BLOCKED WITH MMTS (METHYL METHANETHIOSULFONATE), LEAVING -S-CH3 ATOMS ON ACTIVE ...CATHEPSIN L WAS BLOCKED WITH MMTS (METHYL METHANETHI | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 1.99 Å3/Da / Density % sol: 38.31 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7 Details: 0.1M Tris-HCl, 16% PEG3000, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: MAR CCD 165 mm / Detector: CCD / Date: Aug 20, 2008 / Details: Collimating and focusing, Pt-coated mirrors |
Radiation | Monochromator: Double Crystal Si111 or White Beam / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.69→50 Å / Num. all: 90358 / Num. obs: 86021 / % possible obs: 95.2 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 1.69→1.72 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.273 / Num. unique all: 2830 / % possible all: 62.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 3KFQ, 1ICF Resolution: 1.71→15.33 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: REFINED INDIVIDUALLY
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Displacement parameters | Biso mean: 18.15 Å2
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Refinement step | Cycle: LAST / Resolution: 1.71→15.33 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.706→1.75 Å
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