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Yorodumi- PDB-5j94: Human cathepsin K mutant C25S in complex with the allosteric effe... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5j94 | |||||||||
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Title | Human cathepsin K mutant C25S in complex with the allosteric effector NSC13345 | |||||||||
Components | Cathepsin K | |||||||||
Keywords | HYDROLASE / cysteine proteases / allosteric regulation | |||||||||
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 / MOLECULAR REPLACEMENT / Resolution: 2.22002456664 Å | |||||||||
Authors | Novinec, M. / Korenc, M. / Lenarcic, B. / Baici, A. | |||||||||
Funding support | Slovenia, 2items
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Citation | Journal: Nat Commun / Year: 2014 Title: A novel allosteric mechanism in the cysteine peptidase cathepsin K discovered by computational methods. Authors: Novinec, M. / Korenc, M. / Caflisch, A. / Ranganathan, R. / Lenarcic, B. / Baici, A. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5j94.cif.gz | 65.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5j94.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 5j94.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/j9/5j94 ftp://data.pdbj.org/pub/pdb/validation_reports/j9/5j94 | HTTPS FTP |
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-Related structure data
Related structure data | 4leg 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: 24539.547 Da / Num. of mol.: 1 / Mutation: C25S Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta-Gami 2 pLysS / References: UniProt: P43235, cathepsin K |
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#2: Chemical | ChemComp-1XF / |
#3: Chemical | ChemComp-SO4 / |
#4: 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: 2.1 Å3/Da / Density % sol: 41.5 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5 Details: 0.2 M ammonium sulfate, 30% PEG 8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: ROTATING ANODE / Type: BRUKER AXS MICROSTAR / Wavelength: 1.5418 Å |
Detector | Type: Bruker Platinum 135 / Detector: CCD / Date: Apr 4, 2013 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.22→49.36 Å / Num. obs: 17003 / % possible obs: 86 % / Redundancy: 1.8 % / Biso Wilson estimate: 8.88670326718 Å2 / Rmerge(I) obs: 0.049 / Net I/σ(I): 13.3 |
Reflection shell | Resolution: 2.22→2.3 Å / Redundancy: 1.3 % / Rmerge(I) obs: 0.102 / % possible all: 90.7 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4LEG 4leg Resolution: 2.22002456664→44.827640747 Å / SU ML: 0.220859271542 / Cross valid method: FREE R-VALUE / σ(F): 1.33785830866 / Phase error: 23.200847567
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 16.2828374542 Å2 | |||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.22002456664→44.827640747 Å
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Refine LS restraints |
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LS refinement shell |
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