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- PDB-8r4x: Structure of Chitinase-3-like protein 1 in complex with inhibitor 30 -

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Basic information

Entry
Database: PDB / ID: 8r4x
TitleStructure of Chitinase-3-like protein 1 in complex with inhibitor 30
ComponentsChitinase-3-like protein 1
KeywordsHYDROLASE / Chitinase-3-like-1 / protein-inhibitor complex
Function / homology
Function and homology information


response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / chitin catabolic process / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / extracellular matrix ...response to interleukin-6 / activation of NF-kappaB-inducing kinase activity / cartilage development / chitin catabolic process / extracellular matrix structural constituent / chitin binding / response to tumor necrosis factor / response to mechanical stimulus / response to interleukin-1 / extracellular matrix / positive regulation of peptidyl-threonine phosphorylation / positive regulation of interleukin-8 production / lung development / specific granule lumen / positive regulation of angiogenesis / cellular response to tumor necrosis factor / carbohydrate binding / carbohydrate metabolic process / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / positive regulation of ERK1 and ERK2 cascade / inflammatory response / apoptotic process / Neutrophil degranulation / perinuclear region of cytoplasm / endoplasmic reticulum / extracellular space / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Chitinase insertion domain superfamily / Chitinase II / Glyco_18 / Glycosyl hydrolases family 18 (GH18) domain profile. / Glycoside hydrolase family 18, catalytic domain / Glycosyl hydrolases family 18 / Glycoside hydrolase superfamily
Similarity search - Domain/homology
: / Chitinase-3-like protein 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.54 Å
AuthorsNowak, E. / Napiorkowska-Gromadzka, A. / Nowotny, M.
Funding supportEuropean Union, 1items
OrganizationGrant numberCountry
European Regional Development FundPOIR.01.01.01-00-0552/16European Union
CitationJournal: J.Med.Chem. / Year: 2024
Title: Structure-Based Discovery of High-Affinity Small Molecule Ligands and Development of Tool Probes to Study the Role of Chitinase-3-Like Protein 1.
Authors: Czestkowski, W. / Krzeminski, L. / Piotrowicz, M.C. / Mazur, M. / Pluta, E. / Andryianau, G. / Koralewski, R. / Matyszewski, K. / Olejniczak, S. / Kowalski, M. / Lisiecka, K. / Koziel, R. / ...Authors: Czestkowski, W. / Krzeminski, L. / Piotrowicz, M.C. / Mazur, M. / Pluta, E. / Andryianau, G. / Koralewski, R. / Matyszewski, K. / Olejniczak, S. / Kowalski, M. / Lisiecka, K. / Koziel, R. / Piwowar, K. / Papiernik, D. / Nowotny, M. / Napiorkowska-Gromadzka, A. / Nowak, E. / Niedzialek, D. / Wieczorek, G. / Siwinska, A. / Rejczak, T. / Jedrzejczak, K. / Mulewski, K. / Olczak, J. / Zaslona, Z. / Golebiowski, A. / Drzewicka, K. / Bartoszewicz, A.
History
DepositionNov 14, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 13, 2024Provider: repository / Type: Initial release
Revision 1.1Mar 27, 2024Group: 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Chitinase-3-like protein 1
B: Chitinase-3-like protein 1
C: Chitinase-3-like protein 1
D: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)175,23832
Polymers170,6974
Non-polymers4,54128
Water25,7611430
1
A: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,95410
Polymers42,6741
Non-polymers1,2799
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8389
Polymers42,6741
Non-polymers1,1648
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,6175
Polymers42,6741
Non-polymers9424
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: Chitinase-3-like protein 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,8298
Polymers42,6741
Non-polymers1,1557
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)109.180, 121.390, 134.300
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
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

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Protein / Sugars , 2 types, 8 molecules ABCD

#1: Protein
Chitinase-3-like protein 1


Mass: 42674.355 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: CHI3L1 / Cell (production host): HEK293 / Production host: Mammalia (mammals) / References: UniProt: P36222
#2: Polysaccharide
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-ROHGlycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 4 types, 1454 molecules

#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 17 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-XZ0 / (2~{S},5~{S})-4-[1-(4-chloranylpyridin-2-yl)piperidin-4-yl]-5-[(4-chlorophenyl)methyl]-2-methyl-morpholine


Mass: 420.375 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C22H27Cl2N3O / Feature type: SUBJECT OF INVESTIGATION
#5: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1430 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.75 Å3/Da / Density % sol: 55.21 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop
Details: PEG 4000, 0.1 M sodium citrate pH 4.6, 0.2 M ammonium sulfate and 0.1 M DTT, 0.01 M yttrium chloride hexahydrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: PETRA III, EMBL c/o DESY / Beamline: P13 (MX1) / Wavelength: 0.976 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 25, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976 Å / Relative weight: 1
ReflectionResolution: 1.54→50 Å / Num. obs: 259748 / % possible obs: 98.9 % / Redundancy: 11.2 % / Biso Wilson estimate: 23.39 Å2 / CC1/2: 0.999 / Net I/σ(I): 14.1
Reflection shellResolution: 1.54→1.63 Å / Num. unique obs: 39317 / CC1/2: 0.648

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Processing

Software
NameVersionClassification
PHENIX(1.19.2_4158: ???)refinement
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.54→36.03 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 22.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.19 2723 1.05 %
Rwork0.1698 --
obs0.17 259415 98.79 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.54→36.03 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11293 0 303 1430 13026
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.01612034
X-RAY DIFFRACTIONf_angle_d1.42416324
X-RAY DIFFRACTIONf_dihedral_angle_d12.9961766
X-RAY DIFFRACTIONf_chiral_restr0.0951758
X-RAY DIFFRACTIONf_plane_restr0.0242080
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.54-1.570.43271250.389611827X-RAY DIFFRACTION87
1.57-1.60.34131350.329512664X-RAY DIFFRACTION94
1.6-1.630.32041410.287613310X-RAY DIFFRACTION98
1.63-1.670.31661450.248613575X-RAY DIFFRACTION100
1.67-1.70.24841440.216413546X-RAY DIFFRACTION100
1.7-1.750.22421420.204613509X-RAY DIFFRACTION100
1.75-1.790.24861440.194413574X-RAY DIFFRACTION100
1.79-1.850.21741450.192813559X-RAY DIFFRACTION100
1.85-1.910.2291440.187713563X-RAY DIFFRACTION100
1.91-1.980.20941440.175113611X-RAY DIFFRACTION100
1.98-2.050.19061450.16913619X-RAY DIFFRACTION100
2.05-2.150.18221430.158313620X-RAY DIFFRACTION100
2.15-2.260.17541440.159213628X-RAY DIFFRACTION100
2.26-2.40.19851460.163813711X-RAY DIFFRACTION100
2.4-2.590.19821450.165813714X-RAY DIFFRACTION100
2.59-2.850.15441460.165313695X-RAY DIFFRACTION100
2.85-3.260.19821460.167313806X-RAY DIFFRACTION100
3.26-4.110.17581480.150213885X-RAY DIFFRACTION100
4.11-36.030.15791510.153414276X-RAY DIFFRACTION100
Refinement TLS params.Method: refined / Origin x: -40.4991 Å / Origin y: 1.1882 Å / Origin z: 33.6015 Å
111213212223313233
T0.1738 Å20.0022 Å2-0.0049 Å2-0.1842 Å20.0042 Å2--0.1819 Å2
L0.3111 °20 °2-0.0108 °2-0.3997 °2-0.0018 °2--0.3029 °2
S0.0035 Å °0.0007 Å °-0.0058 Å °0.0027 Å °-0.0071 Å °0.0062 Å °-0.0041 Å °-0.0559 Å °0.0044 Å °
Refinement TLS groupSelection details: all

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