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- PDB-8z25: Crystal structure of mouse Galectin-3 in complex with small molec... -

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Basic information

Entry
Database: PDB / ID: 8z25
TitleCrystal structure of mouse Galectin-3 in complex with small molecule inhibitor
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Fibrosis / Galactose
Function / homology
Function and homology information


negative regulation of NK T cell activation / mononuclear cell migration / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / mononuclear cell migration / negative regulation of immunological synapse formation / disaccharide binding / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / RUNX2 regulates genes involved in differentiation of myeloid cells / regulation of T cell apoptotic process / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / signaling receptor inhibitor activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / secretory granule membrane / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / carbohydrate binding / protein phosphatase binding / : / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / plasma membrane / cytosol / cytoplasm
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.72 Å
AuthorsAmit, K. / Swetha, R. / Ghosh, K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: J.Med.Chem. / Year: 2024
Title: Atropisomerism Observed in Galactose-Based Monosaccharide Inhibitors of Galectin-3 Comprising 2-Methyl-4-phenyl-2,4-dihydro-3 H -1,2,4-triazole-3-thione.
Authors: Yoon, D.S. / Liu, C. / Jalagam, P.R. / Feng, J. / Wang, W. / Swidorski, J.J. / Xu, L. / Hartz, R.A. / Nair, S.K. / Beno, B.R. / Panda, M. / Ghosh, K. / Kumar, A. / Sale, H. / Shah, D. / ...Authors: Yoon, D.S. / Liu, C. / Jalagam, P.R. / Feng, J. / Wang, W. / Swidorski, J.J. / Xu, L. / Hartz, R.A. / Nair, S.K. / Beno, B.R. / Panda, M. / Ghosh, K. / Kumar, A. / Sale, H. / Shah, D. / Mathur, A. / Ellsworth, B.A. / Cheng, D. / Regueiro-Ren, A.
History
DepositionApr 12, 2024Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,0703
Polymers19,3481
Non-polymers7222
Water1,964109
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-3 kcal/mol
Surface area7550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.647, 57.213, 61.784
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Galectin-3 / Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / ...Gal-3 / 35 kDa lectin / Carbohydrate-binding protein 35 / CBP 35 / Galactose-specific lectin 3 / Galactoside-binding protein / GALBP / IgE-binding protein / L-31 / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 19347.986 Da / Num. of mol.: 1 / Mutation: P106H,Y107M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21 (bacteria) / References: UniProt: P17931
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-A1L0R / 5-[(2~{S},3~{R},4~{R},5~{R},6~{R})-4-[4-[4-bromanyl-2,3-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]-4-[5-chloranyl-2-(trifluoromethyl)phenyl]-2-methyl-1,2,4-triazole-3-thione


Mass: 697.859 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19BrClF5N6O4S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 109 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.63 Å3/Da / Density % sol: 24.45 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 0.1M TRIS (7.8), NASCN, PEG 6000

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SEALED TUBE / Type: BRUKER IMUS MICROFOCUS / Wavelength: 1.5 Å
DetectorType: Bruker PHOTON II / Detector: PIXEL / Date: Jul 13, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5 Å / Relative weight: 1
ReflectionResolution: 1.65→27.2 Å / Num. obs: 15153 / % possible obs: 95.9 % / Redundancy: 1.8 % / CC1/2: 0.99 / Net I/σ(I): 6
Reflection shellResolution: 1.65→1.68 Å / Num. unique obs: 511 / CC1/2: 0.7

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Processing

Software
NameVersionClassification
BUSTER2.11.7refinement
iMOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.72→23.34 Å / Cor.coef. Fo:Fc: 0.89 / Cor.coef. Fo:Fc free: 0.848 / SU R Cruickshank DPI: 0.136 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.145 / SU Rfree Blow DPI: 0.133 / SU Rfree Cruickshank DPI: 0.128
RfactorNum. reflection% reflectionSelection details
Rfree0.241 675 5.02 %RANDOM
Rwork0.201 ---
obs0.203 13441 96.2 %-
Displacement parametersBiso mean: 17.87 Å2
Baniso -1Baniso -2Baniso -3
1--14.5265 Å20 Å20 Å2
2--8.2617 Å20 Å2
3---6.2648 Å2
Refine analyzeLuzzati coordinate error obs: 0.27 Å
Refinement stepCycle: 1 / Resolution: 1.72→23.34 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 43 109 1257
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.011203HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.151659HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d411SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes237HARMONIC5
X-RAY DIFFRACTIONt_it1203HARMONIC20
X-RAY DIFFRACTIONt_nbd1SEMIHARMONIC5
X-RAY DIFFRACTIONt_omega_torsion4.36
X-RAY DIFFRACTIONt_other_torsion16.28
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion150SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1294SEMIHARMONIC4
LS refinement shellResolution: 1.72→1.74 Å / Total num. of bins used: 33
RfactorNum. reflection% reflection
Rfree0.361 -5.39 %
Rwork0.2908 386 -
all0.2938 408 -
obs--74.26 %

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