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Yorodumi- PDB-6jjr: Crystal structure of human chitotriosidase-1 (hChit1) catalytic d... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6jjr | ||||||
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Title | Crystal structure of human chitotriosidase-1 (hChit1) catalytic domain in complex with compound 2-8-14 | ||||||
Components | Chitotriosidase-1 | ||||||
Keywords | HYDROLASE / chitinase / complex / chitotriosidase | ||||||
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 / MOLECULAR REPLACEMENT / Resolution: 1.834 Å | ||||||
Authors | Jiang, X. / Yang, Q. | ||||||
Funding support | China, 1items
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Citation | Journal: J.Med.Chem. / Year: 2020 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: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6jjr.cif.gz | 97.9 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6jjr.ent.gz | 71.4 KB | Display | PDB format |
PDBx/mmJSON format | 6jjr.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/jj/6jjr ftp://data.pdbj.org/pub/pdb/validation_reports/jj/6jjr | HTTPS FTP |
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-Related structure data
Related structure data | 6jk6C 6jk9C 6jkfC 6jmnC 4wk9S S: Starting model for refinement C: citing same article (ref.) |
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Similar 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: 42668.734 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Plasmid: pPIC9 / Production host: Pichia (fungus) / Strain (production host): GS115 / References: UniProt: Q13231, chitinase |
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#2: Chemical | ChemComp-BU0 / |
#3: 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: 2.24 Å3/Da / Density % sol: 45.21 % |
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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: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97778 Å |
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: 1.81→43.081 Å / Num. obs: 33762 / % possible obs: 85.06 % / Redundancy: 6 % / Rsym value: 0.085 / Net I/σ(I): 15.17 |
Reflection shell | Resolution: 1.81→1.84 Å / Mean I/σ(I) obs: 1.81 / Num. unique obs: 1583 / Rsym value: 0.772 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 4WK9 Resolution: 1.834→43.081 Å / SU ML: 0.16 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19.48 / Stereochemistry target values: ML
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.834→43.081 Å
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Refine LS restraints |
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LS refinement shell |
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