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Yorodumi- PDB-5nr8: Crystal structure of human chitotriosidase-1 (hCHIT) catalytic do... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5nr8 | ||||||
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Title | Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 7a | ||||||
Components | Chitotriosidase-1 | ||||||
Keywords | HYDROLASE / chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 7a | ||||||
Function / homology | Function and homology information endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...endochitinase activity / polysaccharide digestion / Digestion of dietary carbohydrate / chitinase / chitinase activity / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium / specific granule lumen / tertiary granule lumen / lysosome / immune response / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.349 Å | ||||||
Authors | Podjarny, A. / Fadel, F. / Golebiowski, A. | ||||||
Citation | Journal: J. Med. Chem. / Year: 2018 Title: Targeting Acidic Mammalian chitinase Is Effective in Animal Model of Asthma. Authors: Mazur, M. / Olczak, J. / Olejniczak, S. / Koralewski, R. / Czestkowski, W. / Jedrzejczak, A. / Golab, J. / Dzwonek, K. / Dymek, B. / Sklepkiewicz, P.L. / Zagozdzon, A. / Noonan, T. / ...Authors: Mazur, M. / Olczak, J. / Olejniczak, S. / Koralewski, R. / Czestkowski, W. / Jedrzejczak, A. / Golab, J. / Dzwonek, K. / Dymek, B. / Sklepkiewicz, P.L. / Zagozdzon, A. / Noonan, T. / Mahboubi, K. / Conway, B. / Sheeler, R. / Beckett, P. / Hungerford, W.M. / Podjarny, A. / Mitschler, A. / Cousido-Siah, A. / Fadel, F. / Golebiowski, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5nr8.cif.gz | 173.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5nr8.ent.gz | 143.4 KB | Display | PDB format |
PDBx/mmJSON format | 5nr8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 5nr8_validation.pdf.gz | 657.4 KB | Display | wwPDB validaton report |
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Full document | 5nr8_full_validation.pdf.gz | 660.5 KB | Display | |
Data in XML | 5nr8_validation.xml.gz | 10.6 KB | Display | |
Data in CIF | 5nr8_validation.cif.gz | 16.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/nr/5nr8 ftp://data.pdbj.org/pub/pdb/validation_reports/nr/5nr8 | 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: 42224.289 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Production host: Homo sapiens (human) / References: UniProt: Q13231, chitinase | ||
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#2: Chemical | ChemComp-95N / | ||
#3: Chemical | ChemComp-GOL / #4: 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: 2.27 Å3/Da / Density % sol: 45.88 % |
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Crystal grow | Temperature: 290 K / Method: vapor diffusion, hanging drop Details: 25% (w/v) polyethylene glycol (PEG) 3350, 200 mM potassium sodium tartrate (PST) at pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 0.8 Å |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Dec 5, 2012 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.8 Å / Relative weight: 1 |
Reflection | Resolution: 1.349→30.09 Å / Num. obs: 83374 / % possible obs: 97.44 % / Redundancy: 6.4 % / Net I/σ(I): 34.08 |
-Processing
Software |
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Refinement | Resolution: 1.349→30 Å / Cross valid method: FREE R-VALUE /
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Refinement step | Cycle: LAST / Resolution: 1.349→30 Å
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