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Yorodumi- PDB-6qlx: Cathepsin-K in complex with fluoro-oxa-azabicyclo[3.3.0]octanyl c... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qlx | ||||||
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Title | Cathepsin-K in complex with fluoro-oxa-azabicyclo[3.3.0]octanyl containing inhibitor | ||||||
Components | Cathepsin K | ||||||
Keywords | HYDROLASE / inhibitor complex / lysosomal cysteine 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 / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.1 Å | ||||||
Authors | Derbyshire, D.J. | ||||||
Citation | Journal: To Be Published Title: Successful development of 3-oxohexahydrofuropyrrole amino acid amides as inhibitors of Cathepsin-K. Authors: Derbyshire, D.J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qlx.cif.gz | 108.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qlx.ent.gz | 86.4 KB | Display | PDB format |
PDBx/mmJSON format | 6qlx.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qlx_validation.pdf.gz | 696.3 KB | Display | wwPDB validaton report |
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Full document | 6qlx_full_validation.pdf.gz | 697.3 KB | Display | |
Data in XML | 6qlx_validation.xml.gz | 13.7 KB | Display | |
Data in CIF | 6qlx_validation.cif.gz | 21.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/6qlx ftp://data.pdbj.org/pub/pdb/validation_reports/ql/6qlx | HTTPS FTP |
-Related 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: 23680.674 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSK, CTSO, CTSO2 / Plasmid: pET16b / Production host: Escherichia coli (E. coli) / References: UniProt: P43235, cathepsin K |
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#2: Chemical | ChemComp-HKH / ~{ |
#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: 2.92 Å3/Da / Density % sol: 57.87 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.1 Details: 25mM ADA pH6.1, 400mM sodium chloride and 20% PEG 5k.mme PH range: 6.0 - 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||
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Diffraction source | Source: SYNCHROTRON / Type: SRS / Wavelength: 1.488 Å | ||||||||||||||||||||||||
Detector | Type: ADSC QUANTUM 4 / Detector: CCD / Date: Apr 19, 2005 | ||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.488 Å / Relative weight: 1 | ||||||||||||||||||||||||
Reflection | Resolution: 2.1→71.2 Å / Num. obs: 14341 / % possible obs: 89.5 % / Redundancy: 3.6 % / CC1/2: 0.957 / Rmerge(I) obs: 0.101 / Rpim(I) all: 0.063 / Rrim(I) all: 0.12 / Net I/σ(I): 9.9 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Phasing
Phasing | Method: molecular replacement | |||||||||
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Phasing MR | Model details: Phaser MODE: MR_AUTO
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.1→71.2 Å / Cor.coef. Fo:Fc: 0.887 / Cor.coef. Fo:Fc free: 0.862 / SU B: 7.366 / SU ML: 0.096 / SU R Cruickshank DPI: 0.2541 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.254 / ESU R Free: 0.205 Details: U VALUES : WITH TLS ADDED HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 83.9 Å2 / Biso mean: 22.475 Å2 / Biso min: 10.01 Å2
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Refinement step | Cycle: final / Resolution: 2.1→71.2 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 2.1→2.155 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
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Refinement TLS params. | Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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