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Yorodumi- PDB-3c9e: Crystal structure of the cathepsin K : chondroitin sulfate complex. -
+Open data
-Basic information
Entry | Database: PDB / ID: 3c9e | |||||||||
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Title | Crystal structure of the cathepsin K : chondroitin sulfate complex. | |||||||||
Components | Cathepsin K | |||||||||
Keywords | HYDROLASE / n:1 cathepsin K : chondroitin sulfate complex / "beads-on-a-string" organization / Lysosome / Protease / Thiol protease | |||||||||
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 / Resolution: 1.8 Å | |||||||||
Authors | Kienetz, M. / Cherney, M.M. / James, M.N.G. / Bromme, D. | |||||||||
Citation | Journal: J.Mol.Biol. / Year: 2008 Title: The crystal and molecular structures of a cathepsin K:chondroitin sulfate complex. Authors: Li, Z. / Kienetz, M. / Cherney, M.M. / James, M.N. / Bromme, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3c9e.cif.gz | 61.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3c9e.ent.gz | 47.2 KB | Display | PDB format |
PDBx/mmJSON format | 3c9e.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/c9/3c9e ftp://data.pdbj.org/pub/pdb/validation_reports/c9/3c9e | 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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Unit cell |
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Components on special symmetry positions |
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Details | Author states that biological assembly contains one chondroitin sulfate molecule and N cathepsin K molecules. Depending on their ratio in solution and the Chondroitin sulfate moleculat weight N can vary from 1 to 20 molecules. |
-Components
#1: Protein | Mass: 23523.480 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Pichia pastoris (fungus) / References: UniProt: P43235, cathepsin K |
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#2: Polysaccharide | 2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2- ...2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid-(1-3)-2-acetamido-2-deoxy-4-O-sulfo-beta-D-galactopyranose-(1-4)-beta-D-glucopyranuronic acid Source method: isolated from a genetically manipulated source |
#3: Chemical | ChemComp-CA / |
#4: Chemical | ChemComp-E64 / |
#5: 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: 2.8 Å3/Da / Density % sol: 56.08 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion, hanging drop / pH: 4.5 Details: Cathepsin K:chondroitin sulfate complex was made at 1:1 ratio. Precipitant contained 30% MPD, 0.1M sodium acetate buffer, 20mM calcium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, ...Details: Cathepsin K:chondroitin sulfate complex was made at 1:1 ratio. Precipitant contained 30% MPD, 0.1M sodium acetate buffer, 20mM calcium chloride, pH 4.5, VAPOR DIFFUSION, HANGING DROP, temperature 295K, VAPOR DIFFUSION, HANGING DROP |
-Data collection
Diffraction source | Source: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.05 Å |
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Detector | Type: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 2, 2002 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.05 Å / Relative weight: 1 |
Reflection | Resolution: 1.8→40 Å / Num. all: 25031 / Num. obs: 25031 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4 % / Rmerge(I) obs: 0.142 / Net I/σ(I): 7.3 |
Reflection shell | Resolution: 1.8→1.9 Å / Redundancy: 4.1 % / Rmerge(I) obs: 0.742 / Mean I/σ(I) obs: 1.9 / % possible all: 99.7 |
-Processing
Software |
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Refinement | Resolution: 1.8→40 Å / σ(F): 0
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Solvent computation | Bsol: 61.68 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 17.098 Å2
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Refinement step | Cycle: LAST / Resolution: 1.8→40 Å
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Refine LS restraints |
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Xplor file |
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