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- PDB-6jk6: Crystal structure of human chitotriosidase-1 (hCHIT) catalytic do... -

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Basic information

Entry
Database: PDB / ID: 6jk6
TitleCrystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound 2-8-s2
ComponentsChitotriosidase-1
KeywordsHYDROLASE / chitnase / 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
Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II ...Chitin-binding domain type 2 / Chitin binding domain / Chitin binding Peritrophin-A domain / Chitin-binding type-2 domain profile. / Chitin binding domain superfamily / Glycosyl hydrolases family 18 (GH18) active site / Glycosyl hydrolases family 18 (GH18) active site signature. / Chitinase insertion domain superfamily / : / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycosyl hydrolases family 18 / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-BV0 / Chitotriosidase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.571 Å
AuthorsJiang, X. / Yang, Q.
Funding support China, 1items
OrganizationGrant numberCountry
National Natural Science Foundation of China (NSFC)31425021 China
CitationJournal: 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
DepositionFeb 27, 2019Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Feb 19, 2020Provider: repository / Type: Initial release
Revision 1.1Feb 26, 2020Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Nov 22, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,5603
Polymers42,6691
Non-polymers8912
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: homology
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)66.726, 66.726, 88.363
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number78
Space group name H-MP43

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Components

#1: Protein Chitotriosidase-1 / Chitinase-1


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: Komagataella phaffii GS115 (fungus) / Strain (production host): GS115 / References: UniProt: Q13231, chitinase
#2: Chemical ChemComp-BV0 / 6-azanyl-11-methyl-2-oxidanylidene-7-[[(2R)-oxolan-2-yl]methyl]-N-(pyridin-3-ylmethyl)-1,9-diaza-7-azoniatricyclo[8.4.0.0^{3,8}]tetradeca-3(8),4,6,9,11,13-hexaene-5-carboxamide


Mass: 445.494 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C24H25N6O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 355 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.31 Å3/Da / Density % sol: 46.64 %
Crystal growTemperature: 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

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NFPSS / Beamline: BL19U1 / Wavelength: 0.97778 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 17, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97778 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 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

Software
NameVersionClassification
PHENIX(1.11.1_2575: ???)refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 4WK9

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
RfactorNum. reflection% reflection
Rfree0.1875 2012 3.74 %
Rwork0.1662 --
obs0.167 53781 99.97 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.571→29.84 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2861 0 66 355 3282
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0093008
X-RAY DIFFRACTIONf_angle_d1.0034085
X-RAY DIFFRACTIONf_dihedral_angle_d15.6151093
X-RAY DIFFRACTIONf_chiral_restr0.058420
X-RAY DIFFRACTIONf_plane_restr0.006524
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5714-1.61070.21471390.19963674X-RAY DIFFRACTION100
1.6107-1.65420.22281470.19313695X-RAY DIFFRACTION100
1.6542-1.70290.221410.18553693X-RAY DIFFRACTION100
1.7029-1.75790.18311420.18163711X-RAY DIFFRACTION100
1.7579-1.82070.23381450.17233671X-RAY DIFFRACTION100
1.8207-1.89360.19451370.17273651X-RAY DIFFRACTION100
1.8936-1.97970.20771430.17453711X-RAY DIFFRACTION100
1.9797-2.08410.21581460.17643721X-RAY DIFFRACTION100
2.0841-2.21470.18841460.16883670X-RAY DIFFRACTION100
2.2147-2.38560.19141400.16623694X-RAY DIFFRACTION100
2.3856-2.62570.17621450.16963714X-RAY DIFFRACTION100
2.6257-3.00540.1881450.16633706X-RAY DIFFRACTION100
3.0054-3.78590.16631430.15013705X-RAY DIFFRACTION100
3.7859-29.840.16561530.15053753X-RAY DIFFRACTION100

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