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

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Basic information

Entry
Database: PDB / ID: 8zuv
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 / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.45 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
DepositionJun 10, 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)17,1143
Polymers16,3811
Non-polymers7332
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area7360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.745, 58.108, 62.963
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: 16380.819 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17931
#2: 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
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 2.05 Å3/Da / Density % sol: 40.05 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: BUFFER = 0.1M TRIS (7.8), SALT= NASCN; PRECIPITANT = PEG 6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SOLEIL / Beamline: PROXIMA 1 / Wavelength: 0.9801 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 31, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9801 Å / Relative weight: 1
ReflectionResolution: 1.45→42.7 Å / Num. obs: 22138 / % possible obs: 90 % / Redundancy: 1 % / CC1/2: 0.8 / Net I/σ(I): 1
Reflection shellResolution: 1.45→1.62 Å / Num. unique obs: 22138 / CC1/2: 0.4

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Processing

Software
NameVersionClassification
BUSTER5.8.0232refinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.45→42.7 Å / Cor.coef. Fo:Fc: 0.971 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.191 / SU ML: 0.046 / Cross valid method: THROUGHOUT / ESU R: 0.073 / ESU R Free: 0.073 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.18544 1093 4.9 %RANDOM
Rwork0.15772 ---
obs0.15909 20995 89.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 17.542 Å2
Baniso -1Baniso -2Baniso -3
1-0.87 Å20 Å20 Å2
2---0.12 Å20 Å2
3----0.75 Å2
Refinement stepCycle: 1 / Resolution: 1.45→42.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 43 201 1349
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121233
X-RAY DIFFRACTIONr_bond_other_d0.0020.0171169
X-RAY DIFFRACTIONr_angle_refined_deg1.7511.71693
X-RAY DIFFRACTIONr_angle_other_deg0.6161.5882681
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.3235154
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.0820.98671
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.22315209
X-RAY DIFFRACTIONr_dihedral_angle_4_deg8.251512
X-RAY DIFFRACTIONr_chiral_restr0.0970.2160
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021543
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02308
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3581.416570
X-RAY DIFFRACTIONr_mcbond_other1.3461.411568
X-RAY DIFFRACTIONr_mcangle_it1.9162.119714
X-RAY DIFFRACTIONr_mcangle_other1.9152.119715
X-RAY DIFFRACTIONr_scbond_it2.661.755663
X-RAY DIFFRACTIONr_scbond_other2.6351.753658
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.9372.55966
X-RAY DIFFRACTIONr_long_range_B_refined11.2219.7411329
X-RAY DIFFRACTIONr_long_range_B_other10.32318.6811279
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.45→1.487 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.29 59 -
Rwork0.23 900 -
obs--52.98 %

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