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- PDB-6ze8: Crystal structure of human chitotriosidase-1 (hCHIT) catalytic do... -

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Basic information

Entry
Database: PDB / ID: 6ze8
TitleCrystal structure of human chitotriosidase-1 (hCHIT) catalytic domain in complex with compound OATD-01
ComponentsChitotriosidase-1
KeywordsHYDROLASE / chitinase / chitin binding
Function / homology
Function and homology information


polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / chitin catabolic process / chitin binding / polysaccharide catabolic process / hydrolase activity, hydrolyzing O-glycosyl compounds / response to bacterium ...polysaccharide digestion / Digestion of dietary carbohydrate / chitinase activity / endochitinase activity / chitinase / 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 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycoside hydrolase superfamily
Similarity search - Domain/homology
Chem-QGB / Chitotriosidase-1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNowotny, M. / Bartlomiejczak, A. / Napiorkowska-Gromadzka, A.
CitationJournal: J.Med.Chem. / Year: 2020
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
DepositionJun 16, 2020Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 11, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 6, 2021Group: 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 1.2Jan 24, 2024Group: 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
Revision 1.3Oct 23, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitotriosidase-1
B: Chitotriosidase-1
C: Chitotriosidase-1
D: Chitotriosidase-1
E: Chitotriosidase-1
F: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)247,28419
Polymers244,7086
Non-polymers2,57513
Water42,6962370
1
A: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1993
Polymers40,7851
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1993
Polymers40,7851
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1993
Polymers40,7851
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,2914
Polymers40,7851
Non-polymers5063
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1993
Polymers40,7851
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: Chitotriosidase-1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)41,1993
Polymers40,7851
Non-polymers4142
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)87.325, 93.744, 281.642
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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Components

#1: Protein
Chitotriosidase-1 / Chitinase-1


Mass: 40784.695 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHIT1 / Plasmid: pCMV2 / Cell line (production host): FreeStyle 293-F / Organ (production host): kidney / Production host: Homo sapiens (human) / References: UniProt: Q13231, chitinase
#2: Chemical
ChemComp-QGB / 5-(4-((2S,5S)-5-(4-chlorobenzyl)-2-methylmorpholino)piperidin-1-yl)-4H-1,2,4-triazol-3-amine / 5-[4-[(2~{S},5~{S})-5-[(4-chlorophenyl)methyl]-2-methyl-morpholin-4-yl]piperidin-1-yl]-1~{H}-1,2,4-triazol-3-amine


Mass: 390.910 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C19H27ClN6O / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical
ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 2370 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationY

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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: 2.36 Å3/Da / Density % sol: 47.78 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 31% (w/v) polyethylene glycol (PEG) 3350, 200 mM potassium sodium tartrate (PST)

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.3 / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Aug 22, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 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 shellResolution: 1.5→1.59 Å / Num. unique obs: 58064 / CC1/2: 0.61 / % possible all: 97.7

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Processing

Software
NameVersionClassification
PHENIX1.16refinement
XDSdata reduction
XDSdata scaling
SHELXSphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1WB0

1wb0


Resolution: 1.5→47.34 Å / Cross valid method: NONE
RfactorNum. reflection% reflection
Rfree0.1679 3871 1.05 %
Rwork0.1227 --
obs0.1232 368652 99.56 %
Displacement parametersBiso mean: 23.62 Å2
Refinement stepCycle: LAST / Resolution: 1.5→47.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms17017 0 174 2370 19561
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013318177
X-RAY DIFFRACTIONf_angle_d1.139924765
X-RAY DIFFRACTIONf_chiral_restr0.09762629
X-RAY DIFFRACTIONf_plane_restr0.00723227
X-RAY DIFFRACTIONf_dihedral_angle_d16.922110753

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