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Yorodumi- PDB-1u9v: Crystal Structure of the Cysteine Protease Human Cathepsin K in C... -
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-Basic information
Entry | Database: PDB / ID: 1u9v | ||||||
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Title | Crystal Structure of the Cysteine Protease Human Cathepsin K in Complex with the Covalent Inhibitor NVP-ABE854 | ||||||
Components | Cathepsin K | ||||||
Keywords | HYDROLASE / SULFHYDRYL PROTEINASE | ||||||
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) | ||||||
Method | X-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 2.2 Å | ||||||
Authors | Cowan-Jacob, S.W. | ||||||
Citation | Journal: J.Med.Chem. / Year: 2004 Title: Novel purine nitrile derived inhibitors of the cysteine protease cathepsin K Authors: Altmann, E. / Cowan-Jacob, S.W. / Missbach, M. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1u9v.cif.gz | 56.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1u9v.ent.gz | 39.7 KB | Display | PDB format |
PDBx/mmJSON format | 1u9v.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1u9v_validation.pdf.gz | 761.7 KB | Display | wwPDB validaton report |
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Full document | 1u9v_full_validation.pdf.gz | 763.5 KB | Display | |
Data in XML | 1u9v_validation.xml.gz | 11 KB | Display | |
Data in CIF | 1u9v_validation.cif.gz | 14.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/u9/1u9v ftp://data.pdbj.org/pub/pdb/validation_reports/u9/1u9v | HTTPS FTP |
-Related structure data
Related structure data | 1u9wC 1u9xC 1memS S: Starting model for refinement C: citing same article (ref.) |
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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: 23737.727 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Cell line (production host): SF21 / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43235, cathepsin K |
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#2: Chemical | ChemComp-IHE / |
#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: 2.36 Å3/Da / Density % sol: 47 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8.7 Details: PEG 4000, Tris, magnesium chloride, pH 8.7, VAPOR DIFFUSION, HANGING DROP, temperature 293K |
-Data collection
Diffraction | Mean temperature: 294 K |
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Diffraction source | Source: ROTATING ANODE / Type: ENRAF-NONIUS FR571 / Wavelength: 1.5418 / Wavelength: 1.5418 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 28, 1999 / Details: MONOCHROMATOR |
Radiation | Monochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.2→35.2 Å / Num. all: 12003 / Num. obs: 12003 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 9.9 % / Rmerge(I) obs: 0.0606 / Rsym value: 0.0606 / Net I/σ(I): 48.76 |
Reflection shell | Resolution: 2.2→2.3 Å / Redundancy: 9.1 % / Rmerge(I) obs: 0.1824 / Mean I/σ(I) obs: 16.6 / Rsym value: 0.1824 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 1MEM Resolution: 2.2→20 Å / Data cutoff high absF: 100000 / Data cutoff low absF: 0.1 / σ(F): 0 / Stereochemistry target values: Engh & Huber
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Displacement parameters | Biso mean: 21.27 Å2 | |||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.2→20 Å
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Refine LS restraints |
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Xplor file | Serial no: 1 / Param file: PARHCSDX.PRO / Topol file: TOPHCSDX.PRO |