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- PDB-6jk6: 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: 6jk6 | ||||||
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Title | Crystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 2-8-s2 | ||||||
![]() | Chitotriosidase-1 | ||||||
![]() | HYDROLASE / chitnase / complex / chitotriosidase | ||||||
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 | ![]() ![]() ![]() | ||||||
![]() | Jiang, X. / Yang, Q. | ||||||
Funding support | ![]()
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![]() | ![]() Title: A Series of Compounds Bearing a Dipyrido-Pyrimidine Scaffold Acting as Novel Human and Insect Pest Chitinase Inhibitors. Authors: Jiang, X. / Kumar, A. / Motomura, Y. / Liu, T. / Zhou, Y. / Moro, K. / Zhang, K.Y.J. / Yang, Q. | ||||||
History |
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Structure visualization
Structure viewer | Molecule: ![]() ![]() |
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Downloads & links
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Download
PDBx/mmCIF format | ![]() | 97.9 KB | Display | ![]() |
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PDB format | ![]() | 71 KB | Display | ![]() |
PDBx/mmJSON format | ![]() | Tree view | ![]() | |
Others | ![]() |
-Validation report
Summary document | ![]() | 964.1 KB | Display | ![]() |
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Full document | ![]() | 968.6 KB | Display | |
Data in XML | ![]() | 19.1 KB | Display | |
Data in CIF | ![]() | 29.1 KB | Display | |
Arichive directory | ![]() ![]() | HTTPS FTP |
-Related structure data
Related structure data | ![]() 6jjrC ![]() 6jk9C ![]() 6jkfC ![]() 6jmnC ![]() 4wk9S S: Starting model for refinement C: citing same article ( |
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Similar structure data |
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Links
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Assembly
Deposited unit | ![]()
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Unit cell |
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Components
#1: Protein | Mass: 42668.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) ![]() ![]() | ||||
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#2: Chemical | #3: Water | ChemComp-HOH / | Has ligand of interest | Y | |
-Experimental details
-Experiment
Experiment | Method: ![]() |
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Sample preparation
Crystal | Density Matthews: 2.31 Å3/Da / Density % sol: 46.64 % |
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Crystal grow | Temperature: 277 K / Method: vapor diffusion, hanging drop / pH: 7.2 Details: 25% (w/v) polyethylene glycol (PEG) 3350, 0.2 M potassium sodium tartrate (PST), pH 7.2 |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: ![]() ![]() |
Detector | Type: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.97778 Å / Relative weight: 1 |
Reflection | Resolution: 1.571→36.838 Å / Num. obs: 53832 / % possible obs: 99.96 % / Redundancy: 7.4 % / Rsym value: 0.057 / Net I/σ(I): 37.03 |
Reflection shell | Resolution: 1.571→1.6 Å / Mean I/σ(I) obs: 16.15 / Num. unique obs: 2678 / Rsym value: 0.133 |
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Processing
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Refinement | Method to determine structure: ![]() Starting model: 4WK9 Resolution: 1.571→29.84 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.39 / Phase error: 18.22
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.571→29.84 Å
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Refine LS restraints |
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LS refinement shell |
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