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

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Basic information

Entry
Database: PDB / ID: 8rrf
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: 1.25 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
DepositionJan 22, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 29, 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)16,3985
Polymers15,7011
Non-polymers6974
Water1,838102
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area530 Å2
ΔGint-17 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.480, 57.320, 61.640
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-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-A1H2M / (2~{R},3~{R},4~{S},5~{R},6~{R})-4-[4-[4-chloranyl-2,3-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-6-[[1-[3-(fluoranylmethyl)oxetan-3-yl]-1,2,3-triazol-4-yl]methyl]-2-(hydroxymethyl)-5-methoxy-oxan-3-ol


Mass: 544.911 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H24ClF3N6O5 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-CL / CHLORIDE ION


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


Mass: 18.015 Da / Num. of mol.: 102 / 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: 1.94 Å3/Da / Density % sol: 36.59 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 1.8 M Ammonium citrate pH 7.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: DECTRIS PILATUS 2M / Detector: PIXEL / Date: Dec 30, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→30.092 Å / Num. obs: 82842 / % possible obs: 98.8 % / Redundancy: 3.37 % / CC1/2: 0.999 / Rrim(I) all: 0.061 / Net I/σ(I): 9.73
Reflection shellResolution: 1.15→1.22 Å / Mean I/σ(I) obs: 0.77 / Num. unique obs: 13022 / CC1/2: 0.26 / Rrim(I) all: 1.7 / % possible all: 95.9

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.25→30.092 Å / Cor.coef. Fo:Fc: 0.972 / Cor.coef. Fo:Fc free: 0.971 / SU B: 2.793 / SU ML: 0.05 / Cross valid method: FREE R-VALUE / ESU R: 0.056 / ESU R Free: 0.051
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1979 1720 4.988 %
Rwork0.1745 32760 -
all0.176 --
obs-34480 99.748 %
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: 15.699 Å2
Baniso -1Baniso -2Baniso -3
1-2.733 Å20 Å2-0 Å2
2---2.705 Å20 Å2
3----0.027 Å2
Refinement stepCycle: LAST / Resolution: 1.25→30.092 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 44 102 1249
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121275
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161191
X-RAY DIFFRACTIONr_angle_refined_deg1.6251.8481750
X-RAY DIFFRACTIONr_angle_other_deg0.51.7652741
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4765158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.304511
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.00310201
X-RAY DIFFRACTIONr_dihedral_angle_6_deg13.7611064
X-RAY DIFFRACTIONr_chiral_restr0.0590.2182
X-RAY DIFFRACTIONr_chiral_restr_other1.4660.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021570
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02316
X-RAY DIFFRACTIONr_nbd_refined0.1830.2165
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1930.2991
X-RAY DIFFRACTIONr_nbtor_refined0.1610.2553
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0780.2600
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.0950.271
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1020.214
X-RAY DIFFRACTIONr_nbd_other0.150.263
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1650.220
X-RAY DIFFRACTIONr_mcbond_it1.8091.556604
X-RAY DIFFRACTIONr_mcbond_other1.8011.551602
X-RAY DIFFRACTIONr_mcangle_it2.8572.795767
X-RAY DIFFRACTIONr_mcangle_other2.8572.796768
X-RAY DIFFRACTIONr_scbond_it2.1851.724671
X-RAY DIFFRACTIONr_scbond_other2.1811.722671
X-RAY DIFFRACTIONr_scangle_it3.5043.108980
X-RAY DIFFRACTIONr_scangle_other3.5013.104980
X-RAY DIFFRACTIONr_lrange_it8.52520.2021295
X-RAY DIFFRACTIONr_lrange_other7.89317.8591276
X-RAY DIFFRACTIONr_rigid_bond_restr1.40932466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.25-1.2820.2591290.2842415X-RAY DIFFRACTION99.4527
1.282-1.3170.311120.262301X-RAY DIFFRACTION99.5462
1.317-1.3560.3781020.2652254X-RAY DIFFRACTION99.6616
1.356-1.3970.296850.2362233X-RAY DIFFRACTION99.7848
1.397-1.4430.2641190.2072127X-RAY DIFFRACTION99.6893
1.443-1.4940.211280.1972045X-RAY DIFFRACTION99.9081
1.494-1.550.2071060.1952002X-RAY DIFFRACTION99.9526
1.55-1.6130.2121210.1821888X-RAY DIFFRACTION100
1.613-1.6840.177920.1721884X-RAY DIFFRACTION100
1.684-1.7660.1791000.1721744X-RAY DIFFRACTION99.9458
1.766-1.8620.184860.1681706X-RAY DIFFRACTION99.7773
1.862-1.9740.183840.1541605X-RAY DIFFRACTION99.8817
1.974-2.110.183870.151497X-RAY DIFFRACTION99.8739
2.11-2.2780.202830.1531417X-RAY DIFFRACTION99.8668
2.278-2.4940.218890.1621283X-RAY DIFFRACTION100
2.494-2.7860.215440.181208X-RAY DIFFRACTION99.8405
2.786-3.2130.21480.1641073X-RAY DIFFRACTION99.4676
3.213-3.9240.18590.153891X-RAY DIFFRACTION99.1649
3.924-5.5050.134240.155738X-RAY DIFFRACTION99.8689
5.505-30.0920.172220.22443X-RAY DIFFRACTION98.1013

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