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- PDB-8s67: Galectin-3 with a small molecule inhibitor -

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Basic information

Entry
Database: PDB / ID: 8s67
TitleGalectin-3 with a small molecule inhibitor
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Inhibitor
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
: / THIOCYANATE ION / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.097 Å
AuthorsMac Sweeney, A. / Sager, C.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: To Be Published
Title: Galectin-3 with a small molecule inhibitor
Authors: Remen, L. / Zumbrunn, C. / Sager, C.P. / Grisostomi, C. / Mac Sweeney, A. / Gatfield, J. / Huehn, E. / Vercauteren, E. / Fournier, E. / Schmidt, G. / Davenport, R. / Iglarz, M. / Nayler, O. / Bolli, M.H.
History
DepositionFeb 26, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Mar 12, 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)16,2563
Polymers15,7011
Non-polymers5552
Water3,153175
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area210 Å2
ΔGint-3 kcal/mol
Surface area7270 Å2
Unit cell
Length a, b, c (Å)36.448, 56.887, 61.153
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 15701.049 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 (E. coli) / References: UniProt: P17931
#2: Chemical ChemComp-A1H5A / (2~{R},3~{R},4~{S},5~{R},6~{R})-6-[(1-~{tert}-butyl-1,2,3-triazol-4-yl)methyl]-2-(hydroxymethyl)-5-methoxy-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-3-ol


Mass: 496.483 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H27F3N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 175 / 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: 2.02 Å3/Da / Density % sol: 39.08 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.4M Sodium malonate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.886 Å
DetectorType: DECTRIS EIGER2 XE CdTe 16M / Detector: PIXEL / Date: Feb 21, 2024
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.886 Å / Relative weight: 1
ReflectionResolution: 1.097→30.708 Å / Num. obs: 51801 / % possible obs: 98 % / Redundancy: 8.8 % / CC1/2: 0.99 / Rrim(I) all: 0.129 / Net I/σ(I): 8.6
Reflection shellResolution: 1.1→1.12 Å / Mean I/σ(I) obs: 2.8 / Num. unique obs: 2590 / CC1/2: 0.828 / Rrim(I) all: 0.847 / % possible all: 79

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
autoPROCdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.097→30.708 Å / Cor.coef. Fo:Fc: 0.975 / Cor.coef. Fo:Fc free: 0.966 / WRfactor Rfree: 0.157 / WRfactor Rwork: 0.139 / SU B: 0.913 / SU ML: 0.02 / Average fsc free: 0.9854 / Average fsc work: 0.9898 / Cross valid method: FREE R-VALUE / ESU R: 0.029 / ESU R Free: 0.029
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1535 2531 4.886 %
Rwork0.1361 49267 -
all0.137 --
obs-51798 98.009 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 8.235 Å2
Baniso -1Baniso -2Baniso -3
1--0.827 Å20 Å2-0 Å2
2--1.144 Å2-0 Å2
3----0.317 Å2
Refinement stepCycle: LAST / Resolution: 1.097→30.708 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 38 175 1316
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0121210
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161152
X-RAY DIFFRACTIONr_angle_refined_deg1.8621.8831654
X-RAY DIFFRACTIONr_angle_other_deg0.6971.8352638
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5785143
X-RAY DIFFRACTIONr_dihedral_angle_2_deg7.033510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.12910193
X-RAY DIFFRACTIONr_dihedral_angle_6_deg16.3761058
X-RAY DIFFRACTIONr_chiral_restr0.1080.2174
X-RAY DIFFRACTIONr_chiral_restr_other0.0370.27
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021438
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02292
X-RAY DIFFRACTIONr_nbd_refined0.2140.2150
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1920.21011
X-RAY DIFFRACTIONr_nbtor_refined0.1740.2567
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.2639
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1330.293
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.120.24
X-RAY DIFFRACTIONr_nbd_other0.1420.235
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1170.224
X-RAY DIFFRACTIONr_mcbond_it2.820.652567
X-RAY DIFFRACTIONr_mcbond_other2.7680.649566
X-RAY DIFFRACTIONr_mcangle_it4.1061.171711
X-RAY DIFFRACTIONr_mcangle_other4.111.172712
X-RAY DIFFRACTIONr_scbond_it4.5910.901643
X-RAY DIFFRACTIONr_scbond_other4.5690.899643
X-RAY DIFFRACTIONr_scangle_it6.6281.554943
X-RAY DIFFRACTIONr_scangle_other6.5931.551943
X-RAY DIFFRACTIONr_lrange_it13.78511.6291280
X-RAY DIFFRACTIONr_lrange_other11.3638.331231
X-RAY DIFFRACTIONr_rigid_bond_restr4.7932362
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.097-1.1250.1981540.1829460.18138520.9790.98380.47770.146
1.125-1.1560.1891850.15933300.16137460.9840.98893.83340.13
1.156-1.1890.1931830.15834210.1636500.9810.98898.73970.126
1.189-1.2260.1791720.14833850.14935640.9770.98999.80360.119
1.226-1.2660.1681780.13432870.13634650.9840.9911000.108
1.266-1.310.1371680.12131330.12233010.990.9921000.1
1.31-1.360.1471740.12430780.12532520.9860.9921000.103
1.36-1.4150.1511490.11529280.11730780.9870.99299.96750.1
1.415-1.4780.1361520.1128380.11229900.9880.9931000.099
1.478-1.550.1241240.10627350.10728590.9910.9941000.098
1.55-1.6340.1311250.10425910.10527160.990.9941000.1
1.634-1.7320.1431150.11625030.11726180.9880.9921000.118
1.732-1.8520.147990.12223160.12324150.9870.9911000.128
1.852-1.9990.121120.11921560.11922680.9930.9921000.129
1.999-2.1890.1311070.12920140.12921210.9890.991000.147
2.189-2.4460.142830.13918400.13919230.9870.9881000.165
2.446-2.8220.17700.16216290.16216990.9830.9841000.197
2.822-3.4480.144880.14913620.14914500.9870.9861000.19
3.448-4.8460.156610.13611040.13711660.9840.98999.91420.185
4.846-30.7080.254320.2096710.2117040.9550.97499.8580.31

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