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- PDB-6ze8: Crystal structure of human chitotriosidase-1 (hCHIT) catalytic do... -
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Open data
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Basic information
Entry | Database: PDB / ID: 6ze8 | ||||||
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Title | Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound OATD-01 | ||||||
![]() | Chitotriosidase-1 | ||||||
![]() | HYDROLASE / chitinase / chitin binding | ||||||
Function / homology | ![]() 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 | ![]() | ||||||
Method | ![]() ![]() ![]() | ||||||
![]() | Nowotny, M. / Bartlomiejczak, A. / Napiorkowska-Gromadzka, A. | ||||||
![]() | ![]() Title: Discovery of OATD-01 , a First-in-Class Chitinase Inhibitor as Potential New Therapeutics for Idiopathic Pulmonary Fibrosis. Authors: Koralewski, R. / Dymek, B. / Mazur, M. / Sklepkiewicz, P. / Olejniczak, S. / Czestkowski, W. / Matyszewski, K. / Andryianau, G. / Niedziejko, P. / Kowalski, M. / Gruza, M. / Borek, B. / ...Authors: Koralewski, R. / Dymek, B. / Mazur, M. / Sklepkiewicz, P. / Olejniczak, S. / Czestkowski, W. / Matyszewski, K. / Andryianau, G. / Niedziejko, P. / Kowalski, M. / Gruza, M. / Borek, B. / Jedrzejczak, K. / Bartoszewicz, A. / Pluta, E. / Rymaszewska, A. / Kania, M. / Rejczak, T. / Piasecka, S. / Mlacki, M. / Mazurkiewicz, M. / Piotrowicz, M. / Salamon, M. / Zagozdzon, A. / Napiorkowska-Gromadzka, A. / Bartlomiejczak, A. / Mozga, W. / Dobrzanski, P. / Dzwonek, K. / Golab, J. / Nowotny, M. / Olczak, J. / Golebiowski, A. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 1009.9 KB | Display | ![]() |
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PDB format | ![]() | 803.3 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 1.9 MB | Display | ![]() |
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Full document | ![]() | 1.9 MB | Display | |
Data in XML | ![]() | 101.3 KB | Display | |
Data in CIF | ![]() | 152.5 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 1wb0S S: Starting model for refinement |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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6 | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 40784.695 Da / Num. of mol.: 6 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() #2: Chemical | ChemComp-QGB / #3: Chemical | ChemComp-NA / #4: Chemical | ChemComp-GOL / | #5: Water | ChemComp-HOH / | Has ligand of interest | Y | |
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-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.36 Å3/Da / Density % sol: 47.78 % |
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Crystal grow | Temperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 31% (w/v) polyethylene glycol (PEG) 3350, 200 mM potassium sodium tartrate (PST) |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() ![]() |
Detector | Type: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.976 Å / Relative weight: 1 |
Reflection | Resolution: 1.5→47.34 Å / Num. obs: 368697 / % possible obs: 99.6 % / Redundancy: 7.3 % / CC1/2: 0.999 / Net I/σ(I): 17.04 |
Reflection shell | Resolution: 1.5→1.59 Å / Num. unique obs: 58064 / CC1/2: 0.61 / % possible all: 97.7 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 1WB0 Resolution: 1.5→47.34 Å / Cross valid method: NONE
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Displacement parameters | Biso mean: 23.62 Å2 | ||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.5→47.34 Å
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Refine LS restraints |
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