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Yorodumi- PDB-6ic6: Human cathepsin-C in complex with cyclopropyl peptidyl nitrile in... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6ic6 | |||||||||
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Title | Human cathepsin-C in complex with cyclopropyl peptidyl nitrile inhibitor 1 | |||||||||
Components | (Dipeptidyl peptidase ...) x 3 | |||||||||
Keywords | HYDROLASE / cathepsin-C / cysteine protease / structure-based drug design / arthritis | |||||||||
Function / homology | Function and homology information dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle ...dipeptidyl-peptidase I / peptidase activator activity involved in apoptotic process / positive regulation of proteolysis involved in protein catabolic process / negative regulation of myelination / positive regulation of microglial cell activation / Cargo concentration in the ER / dipeptidyl-peptidase activity / COPII-mediated vesicle transport / chloride ion binding / COPII-coated ER to Golgi transport vesicle / phosphatase binding / cysteine-type peptidase activity / MHC class II antigen presentation / endoplasmic reticulum-Golgi intermediate compartment membrane / : / proteolysis involved in protein catabolic process / positive regulation of apoptotic signaling pathway / T cell mediated cytotoxicity / : / azurophil granule lumen / protein-folding chaperone binding / collagen-containing extracellular matrix / lysosome / immune response / endoplasmic reticulum lumen / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / centrosome / Neutrophil degranulation / proteolysis / extracellular space / extracellular exosome / extracellular region / nucleoplasm / identical protein binding / membrane Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.898 Å | |||||||||
Authors | Hakansson, M. / Logan, D.T. / Korkmaz, B. / Lesner, A. / Wysocka, M. / Gieldon, A. / Gauthier, F. / Jenne, D. / Lauritzen, C. / Pedersen, J. | |||||||||
Funding support | Poland, 1items
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Citation | Journal: Biochem. Pharmacol. / Year: 2019 Title: Structure-based design and in vivo anti-arthritic activity evaluation of a potent dipeptidyl cyclopropyl nitrile inhibitor of cathepsin C. Authors: Korkmaz, B. / Lesner, A. / Wysocka, M. / Gieldon, A. / Hakansson, M. / Gauthier, F. / Logan, D.T. / Jenne, D.E. / Lauritzen, C. / Pedersen, J. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6ic6.cif.gz | 156.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6ic6.ent.gz | 117.5 KB | Display | PDB format |
PDBx/mmJSON format | 6ic6.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6ic6_validation.pdf.gz | 1 MB | Display | wwPDB validaton report |
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Full document | 6ic6_full_validation.pdf.gz | 1 MB | Display | |
Data in XML | 6ic6_validation.xml.gz | 20 KB | Display | |
Data in CIF | 6ic6_validation.cif.gz | 28.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ic/6ic6 ftp://data.pdbj.org/pub/pdb/validation_reports/ic/6ic6 | 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
-Dipeptidyl peptidase ... , 3 types, 3 molecules ABC
#1: Protein | Mass: 13500.163 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I |
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#2: Protein | Mass: 18630.018 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I |
#3: Protein | Mass: 7583.444 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CTSC, CPPI / Cell line (production host): BTI-TN-5B1-4 / Production host: Trichoplusia ni (cabbage looper) / References: UniProt: P53634, dipeptidyl-peptidase I |
-Sugars , 2 types, 3 molecules
#4: Polysaccharide | alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2- ...alpha-D-mannopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose Source method: isolated from a genetically manipulated source |
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#5: Sugar |
-Non-polymers , 3 types, 298 molecules
#6: Chemical | ChemComp-CL / |
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#7: Chemical | ChemComp-H9B / ( |
#8: 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: 2.79 Å3/Da / Density % sol: 55.9 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5 / Details: 20.0 % (w/v) PEG 6000 0.1 M sodium citrate pH 5.0 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.03796 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Dec 10, 2009 |
Radiation | Monochromator: DOUBLE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.03796 Å / Relative weight: 1 |
Reflection | Resolution: 1.898→28.026 Å / Num. obs: 34042 / % possible obs: 97.2 % / Redundancy: 3.7 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 18.4 |
Reflection shell | Resolution: 1.898→1.95 Å / Rmerge(I) obs: 0.394 / Mean I/σ(I) obs: 3.4 / % possible all: 96 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: in-house structure Resolution: 1.898→28.026 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.952 / SU B: 5.154 / SU ML: 0.077 / Cross valid method: THROUGHOUT / ESU R: 0.116 / ESU R Free: 0.114 / Details: Hydrogens were added in their 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 mean: 27.472 Å2
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Refinement step | Cycle: LAST / Resolution: 1.898→28.026 Å
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Refine LS restraints |
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LS refinement shell | Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20
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Refinement TLS params. | Details: U values: with tls added / Method: refined / Refine-ID: X-RAY DIFFRACTION
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Refinement TLS group |
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