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Yorodumi- PDB-6hgy: CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C -
+Open data
-Basic information
Entry | Database: PDB / ID: 6hgy | ||||||
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Title | CRYSTAL STRUCTURE OF CATHEPSIN K WITH N-DESMETHYL THALASSOSPIRAMIDE C | ||||||
Components | Cathepsin K | ||||||
Keywords | HYDROLASE / PROTEASE / CATHEPSIN K / PROTEROS BIOSTRUCTURES GMBH | ||||||
Function / homology | Function and homology information cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding ...cathepsin K / mononuclear cell differentiation / intramembranous ossification / negative regulation of cartilage development / cellular response to zinc ion starvation / RUNX1 regulates transcription of genes involved in differentiation of keratinocytes / thyroid hormone generation / endolysosome lumen / Trafficking and processing of endosomal TLR / proteoglycan binding / Activation of Matrix Metalloproteinases / cysteine-type endopeptidase activator activity involved in apoptotic process / mitophagy / fibronectin binding / Collagen degradation / collagen catabolic process / extracellular matrix disassembly / bone resorption / cysteine-type peptidase activity / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / response to insulin / response to organic cyclic compound / cellular response to tumor necrosis factor / response to ethanol / lysosome / immune response / apical plasma membrane / external side of plasma membrane / cysteine-type endopeptidase activity / serine-type endopeptidase activity / intracellular membrane-bounded organelle / proteolysis / extracellular space / extracellular region / nucleoplasm Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Zakarian, A. / Buckman, B.O. / Adler, M. / Griessner, A. / Blaesse, M. | ||||||
Citation | Journal: Org.Lett. / Year: 2019 Title: Total Synthesis of Covalent Cysteine Protease Inhibitor N-Desmethyl Thalassospiramide C and Crystallographic Evidence for Its Mode of Action. Authors: Fournier, J. / Chen, K. / Mailyan, A.K. / Jackson, J.J. / Buckman, B.O. / Emayan, K. / Yuan, S. / Rajagopalan, R. / Misialek, S. / Adler, M. / Blaesse, M. / Griessner, A. / Zakarian, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6hgy.cif.gz | 99.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6hgy.ent.gz | 75 KB | Display | PDB format |
PDBx/mmJSON format | 6hgy.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/hg/6hgy ftp://data.pdbj.org/pub/pdb/validation_reports/hg/6hgy | HTTPS FTP |
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-Related structure data
Related structure data | 1atkS S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 23523.480 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K |
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#2: Chemical | ChemComp-G4B / |
#3: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.9 Å3/Da / Density % sol: 35.33 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion / Details: 0.05M MES pH 6.0, 0.1M Na-Oxalate, 0.1M CaCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99992 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Sep 3, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.99992 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→44.97 Å / Num. obs: 8527 / % possible obs: 86.9 % / Observed criterion σ(I): 0 / Redundancy: 3.8 % / Rmerge(I) obs: 0.114 / Net I/σ(I): 7.69 |
Reflection shell | Resolution: 2.2→2.42 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.425 / % possible all: 77.8 |
-Processing
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 1ATK Resolution: 2.2→44.97 Å / Cor.coef. Fo:Fc: 0.918 / Cor.coef. Fo:Fc free: 0.88 / SU B: 26.965 / SU ML: 0.316 / Cross valid method: THROUGHOUT / ESU R: 3.557 / ESU R Free: 0.378 / 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 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 40.45 Å2
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Refinement step | Cycle: LAST / Resolution: 2.2→44.97 Å
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Refine LS restraints |
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