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Yorodumi- PDB-3iej: Pyrazole-based Cathepsin S Inhibitors with Arylalkynes as P1 Bind... -
+Open data
-Basic information
Entry | Database: PDB / ID: 3iej | ||||||
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Title | Pyrazole-based Cathepsin S Inhibitors with Arylalkynes as P1 Binding Elements | ||||||
Components | Cathepsin S | ||||||
Keywords | HYDROLASE / CATHEPSIN S / Disulfide bond / Glycoprotein / Lysosome / Polymorphism / Protease / Thiol protease / Zymogen | ||||||
Function / homology | Function and homology information cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures ...cathepsin S / basement membrane disassembly / positive regulation of cation channel activity / antigen processing and presentation of peptide antigen / endolysosome lumen / response to acidic pH / cellular response to thyroid hormone stimulus / Trafficking and processing of endosomal TLR / proteoglycan binding / Assembly of collagen fibrils and other multimeric structures / toll-like receptor signaling pathway / antigen processing and presentation / cysteine-type endopeptidase activator activity involved in apoptotic process / fibronectin binding / collagen catabolic process / extracellular matrix disassembly / laminin binding / collagen binding / MHC class II antigen presentation / phagocytic vesicle / Degradation of the extracellular matrix / lysosomal lumen / proteolysis involved in protein catabolic process / Endosomal/Vacuolar pathway / positive regulation of apoptotic signaling pathway / protein processing / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / tertiary granule lumen / collagen-containing extracellular matrix / adaptive immune response / ficolin-1-rich granule lumen / lysosome / immune response / cysteine-type endopeptidase activity / intracellular membrane-bounded organelle / serine-type endopeptidase activity / Neutrophil degranulation / proteolysis / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / OTHER / Resolution: 2.18 Å | ||||||
Authors | Bembenek, S. | ||||||
Citation | Journal: Bioorg.Med.Chem.Lett. / Year: 2009 Title: Pyrazole-based cathepsin S inhibitors with arylalkynes as P1 binding elements. Authors: Ameriks, M.K. / Axe, F.U. / Bembenek, S.D. / Edwards, J.P. / Gu, Y. / Karlsson, L. / Randal, M. / Sun, S. / Thurmond, R.L. / Zhu, J. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 3iej.cif.gz | 97.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb3iej.ent.gz | 79.8 KB | Display | PDB format |
PDBx/mmJSON format | 3iej.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 3iej_validation.pdf.gz | 919.8 KB | Display | wwPDB validaton report |
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Full document | 3iej_full_validation.pdf.gz | 927.1 KB | Display | |
Data in XML | 3iej_validation.xml.gz | 20.8 KB | Display | |
Data in CIF | 3iej_validation.cif.gz | 28.8 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ie/3iej ftp://data.pdbj.org/pub/pdb/validation_reports/ie/3iej | HTTPS FTP |
-Related structure data
Similar structure data |
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-Links
-Assembly
Deposited unit |
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2 |
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Unit cell |
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Noncrystallographic symmetry (NCS) | NCS domain:
NCS domain segments:
NCS oper: (Code: given Matrix: (-0.9924, 0.008117, 0.1225), Vector: |
-Components
#1: Protein | Mass: 24431.367 Da / Num. of mol.: 2 / Mutation: C25S Source method: isolated from a genetically manipulated source Details: JNJ27120509 / Source: (gene. exp.) Homo sapiens (human) / Gene: CTSS / Production host: Escherichia coli (E. coli) / References: UniProt: P25774, cathepsin S #2: Chemical | #3: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43.12 % |
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Crystal grow | pH: 4.56 / Details: pH 4.56 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.97949 |
Detector | Type: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 8, 2008 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97949 Å / Relative weight: 1 |
Reflection | Resolution: 2.15→100.5 Å / Num. obs: 20453 / % possible obs: 92.4 % / Observed criterion σ(I): 0 / Redundancy: 3 % / Rmerge(I) obs: 0.17 / Net I/σ(I): 5.6 |
-Processing
Software |
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Refinement | Method to determine structure: OTHER / Resolution: 2.18→50 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.879 / SU B: 6.75 / SU ML: 0.174 / Cross valid method: THROUGHOUT / ESU R: 0.383 / ESU R Free: 0.262 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: 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 / Solvent model: MASK | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 13.905 Å2
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Refinement step | Cycle: LAST / Resolution: 2.18→50 Å
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Refine LS restraints |
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Refine LS restraints NCS | Dom-ID: 1 / Auth asym-ID: B / Ens-ID: 1 / Number: 2884 / Refine-ID: X-RAY DIFFRACTION
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LS refinement shell | Resolution: 2.18→2.234 Å / Total num. of bins used: 20 /
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