+Open data
-Basic information
Entry | Database: PDB / ID: 3kwb | ||||||
---|---|---|---|---|---|---|---|
Title | Structure of CatK covalently bound to a dioxo-triazine inhibitor | ||||||
Components | Cathepsin K | ||||||
Keywords | HYDROLASE / covalent bond / Cys 25 / thioimidate / Disease mutation / Disulfide bond / Glycoprotein / Lysosome / Protease / Thiol protease / Zymogen | ||||||
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 / Collagen degradation / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / cysteine-type peptidase activity / positive regulation of apoptotic signaling pathway / bone resorption / cellular response to transforming growth factor beta stimulus / collagen binding / MHC class II antigen presentation / Degradation of the extracellular matrix / proteolysis involved in protein catabolic process / lysosomal lumen / 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: 2.02 Å | ||||||
Authors | Uitdehaag, J.C.M. / van Zeeland, M. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2010 Title: Dioxo-triazines as a novel series of cathepsin K inhibitors Authors: Rankovic, Z. / Cai, J. / Fradera, X. / Dempster, M. / Mistry, A. / Mitchell, A. / Long, C. / Hamilton, E. / King, A. / Boucharens, S. / Jamieson, C. / Gillespie, J. / Cumming, I. / ...Authors: Rankovic, Z. / Cai, J. / Fradera, X. / Dempster, M. / Mistry, A. / Mitchell, A. / Long, C. / Hamilton, E. / King, A. / Boucharens, S. / Jamieson, C. / Gillespie, J. / Cumming, I. / Uitdehaag, J. / van Zeeland, M. | ||||||
History |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 3kwb.cif.gz | 105.6 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb3kwb.ent.gz | 84.3 KB | Display | PDB format |
PDBx/mmJSON format | 3kwb.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/kw/3kwb ftp://data.pdbj.org/pub/pdb/validation_reports/kw/3kwb | HTTPS FTP |
---|
-Related structure data
Related structure data | |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
2 |
| ||||||||
Unit cell |
|
-Components
#1: Protein | Mass: 23523.480 Da / Num. of mol.: 2 / Fragment: full length / Mutation: wild type Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Organ (production host): ovary / Production host: Cricetulus griseus (Chinese hamster) / References: UniProt: P43235, cathepsin K #2: Chemical | #3: Water | ChemComp-HOH / | |
---|
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.08 Å3/Da / Density % sol: 40.88 % |
---|---|
Crystal grow | Temperature: 298 K / pH: 3.4 Details: 30%(W/V) PEG 4000 and 150 mM Ammonium Sulfate pH 3.4 3 microliter of protein at 10 mg/ml and 2 microliter of reservoir solution. , VAPOR DIFFUSION, HANGING DROP, temperature 298K |
-Data collection
Diffraction | Mean temperature: 100 K |
---|---|
Diffraction source | Source: ROTATING ANODE / Type: RIGAKU / Wavelength: 1.5418 |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 13, 2004 / Details: MIRRORS |
Radiation | Monochromator: UNKNOWN / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.5418 Å / Relative weight: 1 |
Reflection | Resolution: 2.017→27.461 Å / Num. obs: 23819 / % possible obs: 93.1 % / Observed criterion σ(I): 0 / Redundancy: 2.3 % / Rmerge(I) obs: 0.068 / Rsym value: 0.068 / Net I/σ(I): 13 |
Reflection shell | Resolution: 2.01→2.12 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.181 / Mean I/σ(I) obs: 4.1 / Rsym value: 0.181 / % possible all: 82.7 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.02→27.47 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.908 / Occupancy max: 1 / Occupancy min: 1 / SU B: 4.329 / SU ML: 0.122 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.296 / ESU R Free: 0.194 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 18.42 Å2
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 2.02→27.47 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell | Resolution: 2.02→2.07 Å / Total num. of bins used: 20
|