+Open data
-Basic information
Entry | Database: PDB / ID: 2auz | ||||||
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Title | Cathepsin K complexed with a semicarbazone inhibitor | ||||||
Components | Cathepsin K | ||||||
Keywords | HYDROLASE / catK / cysteine 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 / 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: 2.3 Å | ||||||
Authors | Adkison, K.K. / Barrett, D.G. / Deaton, D.N. / Gampe, R.T. / Hassell, A.M. / Long, S.T. / McFadyen, R.B. / Miller, A.B. / Miller, L.R. / Shewchuk, L.M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2006 Title: Semicarbazone-based inhibitors of cathepsin K, are they prodrugs for aldehyde inhibitors? Authors: Adkison, K.K. / Barrett, D.G. / Deaton, D.N. / Gampe, R.T. / Hassell, A.M. / Long, S.T. / McFadyen, R.B. / Miller, A.B. / Miller, L.R. / Payne, J.A. / Shewchuk, L.M. / Wells-Knecht, K.J. / ...Authors: Adkison, K.K. / Barrett, D.G. / Deaton, D.N. / Gampe, R.T. / Hassell, A.M. / Long, S.T. / McFadyen, R.B. / Miller, A.B. / Miller, L.R. / Payne, J.A. / Shewchuk, L.M. / Wells-Knecht, K.J. / Willard, D.H. / Wright, L.L. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2auz.cif.gz | 58.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2auz.ent.gz | 42.3 KB | Display | PDB format |
PDBx/mmJSON format | 2auz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2auz_validation.pdf.gz | 777.7 KB | Display | wwPDB validaton report |
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Full document | 2auz_full_validation.pdf.gz | 779.5 KB | Display | |
Data in XML | 2auz_validation.xml.gz | 12 KB | Display | |
Data in CIF | 2auz_validation.cif.gz | 16.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/au/2auz ftp://data.pdbj.org/pub/pdb/validation_reports/au/2auz | HTTPS FTP |
-Related structure data
Related structure data | 2auxC 1atkS 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: mature form of cathepsin K (residues 115-329) Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Plasmid: pFastbac / Production host: Spodoptera frugiperda (fall armyworm) / References: UniProt: P43235, cathepsin K | ||||
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#2: Chemical | #3: Chemical | ChemComp-CT2 / | #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: 2.2 Å3/Da / Density % sol: 44 % |
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Crystal grow | Method: vapor diffusion, sitting drop / pH: 5.5 Details: 0.2M ammonium sulfate, 30% PEG8000, pH 5.5, VAPOR DIFFUSION, SITTING DROP |
-Data collection
Diffraction | Mean temperature: 200 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.54 Å |
Detector | Type: RIGAKU RAXIS II / Detector: IMAGE PLATE / Date: Jun 12, 1998 / Details: mirrors |
Radiation | Monochromator: mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.54 Å / Relative weight: 1 |
Reflection | Resolution: 2.3→52 Å / Num. all: 9442 / Num. obs: 9442 / % possible obs: 95.1 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2 / Redundancy: 4.7 % / Rmerge(I) obs: 0.053 / Net I/σ(I): 37 |
Reflection shell | Resolution: 2.3→2.38 Å / Redundancy: 3 % / Rmerge(I) obs: 0.112 / Mean I/σ(I) obs: 14 / Num. unique all: 850 / % possible all: 88.4 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB entry 1ATK Resolution: 2.3→52 Å / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / σ(F): 2 / σ(I): 2 / Stereochemistry target values: Engh & Huber / Details: mask method used for bulk solvent correction
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Refinement step | Cycle: LAST / Resolution: 2.3→52 Å
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Refine LS restraints |
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