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Yorodumi- PDB-4yv8: Crystal structure of cathepsin K bound to the covalent inhibitor ... -
+Open data
-Basic information
Entry | Database: PDB / ID: 4yv8 | |||||||||
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Title | Crystal structure of cathepsin K bound to the covalent inhibitor lichostatinal | |||||||||
Components |
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Keywords | HYDROLASE/INHIBITOR / cathepsin K / lichostatinal / inhibitor / HYDROLASE-INHIBITOR complex | |||||||||
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 / cysteine-type peptidase activity / bone resorption / 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 / intracellular membrane-bounded organelle / serine-type endopeptidase activity / proteolysis / extracellular space / extracellular region / nucleoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) actinomycete 095-35 (bacteria) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å | |||||||||
Authors | Aguda, A.H. / Nguyen, N.T. / Bromme, D. / Brayer, G.D. | |||||||||
Funding support | Canada, 1items
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Citation | Journal: J.Nat.Prod. / Year: 2016 Title: Affinity Crystallography: A New Approach to Extracting High-Affinity Enzyme Inhibitors from Natural Extracts. Authors: Aguda, A.H. / Lavallee, V. / Cheng, P. / Bott, T.M. / Meimetis, L.G. / Law, S. / Nguyen, N.T. / Williams, D.E. / Kaleta, J. / Villanueva, I. / Davies, J. / Andersen, R.J. / Brayer, G.D. / Bromme, D. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4yv8.cif.gz | 61.4 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4yv8.ent.gz | 42.8 KB | Display | PDB format |
PDBx/mmJSON format | 4yv8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4yv8_validation.pdf.gz | 446.6 KB | Display | wwPDB validaton report |
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Full document | 4yv8_full_validation.pdf.gz | 447.1 KB | Display | |
Data in XML | 4yv8_validation.xml.gz | 11.9 KB | Display | |
Data in CIF | 4yv8_validation.cif.gz | 16.9 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/yv/4yv8 ftp://data.pdbj.org/pub/pdb/validation_reports/yv/4yv8 | HTTPS FTP |
-Related structure data
Related structure data | 4yvaC 3c9eS C: citing same article (ref.) 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: UNP residues 115-329 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Production host: Pichia (fungus) / References: UniProt: P43235, cathepsin K | ||
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#2: Protein/peptide | | ||
#3: Chemical | #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: 2.18 Å3/Da / Density % sol: 43.59 % |
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Crystal grow | Temperature: 294.15 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 24% PEG 8000, 0.2M ammonium sulfate |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97 Å |
Detector | Type: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Feb 13, 2010 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97 Å / Relative weight: 1 |
Reflection | Resolution: 2→38.332 Å / Num. obs: 15131 / % possible obs: 99.7 % / Redundancy: 8.9 % / Rmerge(I) obs: 0.074 / Net I/σ(I): 18.9 |
Reflection shell | Highest resolution: 2 Å / Redundancy: 9.2 % / Rmerge(I) obs: 0.28 / Mean I/σ(I) obs: 7.7 / % possible all: 100 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3C9E Resolution: 2→38.33 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 0.69 / Phase error: 18.16 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | ||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2→38.33 Å
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Refine LS restraints |
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LS refinement shell |
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