+Open data
-Basic information
Entry | Database: PDB / ID: 3hwn | ||||||
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Title | CATHEPSIN L with AZ13010160 | ||||||
Components | Cathepsin L1 | ||||||
Keywords | HYDROLASE / Cathepsin L / Drug Design / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen | ||||||
Function / homology | Function and homology information enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus ...enkephalin processing / cathepsin L / CD4-positive, alpha-beta T cell lineage commitment / macrophage apoptotic process / chromaffin granule / elastin catabolic process / antigen processing and presentation of peptide antigen / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / endolysosome lumen / cellular response to thyroid hormone stimulus / zymogen activation / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / cysteine-type endopeptidase activator activity involved in apoptotic process / protein autoprocessing / fibronectin binding / Collagen degradation / antigen processing and presentation / collagen catabolic process / serpin family protein binding / Attachment and Entry / positive regulation of apoptotic signaling pathway / cysteine-type peptidase activity / endocytic vesicle lumen / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / multivesicular body / proteolysis involved in protein catabolic process / lysosomal lumen / Endosomal/Vacuolar pathway / antigen processing and presentation of exogenous peptide antigen via MHC class II / histone binding / collagen-containing extracellular matrix / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / adaptive immune response / lysosome / immune response / symbiont entry into host cell / 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 / nucleus / plasma membrane Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.33 Å | ||||||
Authors | Kenny, P. / Morley, A. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Design of selective Cathepsin inhibitors Authors: Bethel, P.A. / Gerhardt, S. / Jones, E.V. / Kenny, P.W. / Karoutchi, G.I. / Morley, A.D. / Oldham, K. / Rankine, N. / Augustin, M. / Krapp, S. / Simader, H. / Steinbacher, S. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3hwn.cif.gz | 176.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3hwn.ent.gz | 146.7 KB | Display | PDB format |
PDBx/mmJSON format | 3hwn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hw/3hwn ftp://data.pdbj.org/pub/pdb/validation_reports/hw/3hwn | HTTPS FTP |
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-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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4 |
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Unit cell |
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-Components
#1: Protein | Mass: 28678.809 Da / Num. of mol.: 4 / Fragment: PROTEASE Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSL1, CTSL / Production host: Escherichia coli (E. coli) / References: UniProt: P07711, cathepsin L #2: Chemical | ChemComp-BD3 / #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: 1.79 Å3/Da / Density % sol: 31.29 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7.4 Details: PEG, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K | |||||||||
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06SA / Wavelength: 1 / Wavelength: 1.0005 Å | |||||||||
Detector | Type: PSI PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2007 / Details: LN2 COOLED FIXED-EXIT | |||||||||
Radiation | Monochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | |||||||||
Radiation wavelength |
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Reflection | Resolution: 2.33→35.81 Å / Num. all: 31595 / Num. obs: 31593 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 2 % / Rmerge(I) obs: 0.098 | |||||||||
Reflection shell | Resolution: 2.33→2.39 Å / Redundancy: 2 % / Rmerge(I) obs: 0.209 / % possible all: 81.9 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.33→35.81 Å / Cor.coef. Fo:Fc: 0.854 / Cor.coef. Fo:Fc free: 0.707 / SU B: 15.084 / SU ML: 0.373 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.871 / ESU R Free: 0.387 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 27.465 Å2
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Refinement step | Cycle: LAST / Resolution: 2.33→35.81 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.334→2.394 Å / Total num. of bins used: 20
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