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Yorodumi- PDB-7qbn: Structure of cathepsin K in complex with the azadipeptide nitrile... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7qbn | |||||||||
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Title | Structure of cathepsin K in complex with the azadipeptide nitrile inhibitor Gu1303 | |||||||||
Components | Cathepsin K | |||||||||
Keywords | HYDROLASE / Cathepsin K / Protease inhibitor / Cyanohydrazide warhead / Azadipeptide nitrile | |||||||||
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: 1.55 Å | |||||||||
Authors | Benysek, J. / Busa, M. / Mares, M. | |||||||||
Funding support | Czech Republic, 2items
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Citation | Journal: J Enzyme Inhib Med Chem / Year: 2022 Title: Highly potent inhibitors of cathepsin K with a differently positioned cyanohydrazide warhead: structural analysis of binding mode to mature and zymogen-like enzymes. Authors: Benysek, J. / Busa, M. / Rubesova, P. / Fanfrlik, J. / Lepsik, M. / Brynda, J. / Matouskova, Z. / Bartz, U. / Horn, M. / Gutschow, M. / Mares, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7qbn.cif.gz | 66.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7qbn.ent.gz | 46 KB | Display | PDB format |
PDBx/mmJSON format | 7qbn.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7qbn_validation.pdf.gz | 799.9 KB | Display | wwPDB validaton report |
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Full document | 7qbn_full_validation.pdf.gz | 799.8 KB | Display | |
Data in XML | 7qbn_validation.xml.gz | 13.1 KB | Display | |
Data in CIF | 7qbn_validation.cif.gz | 20.3 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qb/7qbn ftp://data.pdbj.org/pub/pdb/validation_reports/qb/7qbn | HTTPS FTP |
-Related structure data
Related structure data | 7qblC 7qbmC 7qboC 7nxmS 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 on special symmetry positions |
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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) / Gene: CTSK, CTSO, CTSO2 / Production host: Komagataella phaffii GS115 (fungus) / References: UniProt: P43235, cathepsin K |
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#2: Chemical | ChemComp-9ZG / ( |
#3: Chemical | ChemComp-CL / |
#4: Chemical | ChemComp-ACT / |
#5: Water | ChemComp-HOH / |
Has ligand of interest | Y |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 1.98 Å3/Da / Density % sol: 37.84 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% MPD, 0.03 M sodium nitrate, 0.03 M disodium hydrogen phosphate, 0.03 M ammonium sulfate, 0.1 M MES/imidazole pH 6.5 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.5419 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Detector | Type: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Feb 28, 2019 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Radiation wavelength | Wavelength: 1.5419 Å / Relative weight: 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection | Resolution: 1.55→37.5 Å / Num. obs: 23646 / % possible obs: 83.4 % / Redundancy: 6.512 % / Biso Wilson estimate: 15.94 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.085 / Rrim(I) all: 0.092 / Χ2: 0.845 / Net I/σ(I): 19.43 / Num. measured all: 153974 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 7NXM Resolution: 1.55→37.5 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.959 / SU B: 1.382 / SU ML: 0.05 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.09 / ESU R Free: 0.084 / Stereochemistry target values: MAXIMUM LIKELIHOOD Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso max: 45.32 Å2 / Biso mean: 13.033 Å2 / Biso min: 7.35 Å2
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Refinement step | Cycle: final / Resolution: 1.55→37.5 Å
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Refine LS restraints |
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LS refinement shell | Resolution: 1.55→1.586 Å / Rfactor Rfree error: 0
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