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- PDB-8rr8: Galectin-3 with a small molecule inhibitor -

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Basic information

Entry
Database: PDB / ID: 8rr8
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 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)16,2462
Polymers15,7011
Non-polymers5451
Water1,04558
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area690 Å2
ΔGint-1 kcal/mol
Surface area7350 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.500, 57.340, 61.950
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-A1H2S / (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~{R},4~{R})-4-fluoranyloxolan-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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 58 / 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: 1.95 Å3/Da / Density % sol: 36.97 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / Details: 2.1 M DL-Malic acid 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: May 5, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→42.081 Å / Num. obs: 37873 / % possible obs: 99.7 % / Redundancy: 3.46 % / CC1/2: 0.998 / Rrim(I) all: 0.081 / Net I/σ(I): 8.66
Reflection shellResolution: 1.5→1.59 Å / Mean I/σ(I) obs: 0.65 / Num. unique obs: 6110 / CC1/2: 0.257 / Rrim(I) all: 2.02

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.5→30.994 Å / Cor.coef. Fo:Fc: 0.976 / Cor.coef. Fo:Fc free: 0.968 / SU B: 5.818 / SU ML: 0.088 / Cross valid method: FREE R-VALUE / ESU R: 0.098 / ESU R Free: 0.083
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2163 1038 5.115 %
Rwork0.166 19256 -
all0.168 --
obs-20294 99.926 %
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: 25.62 Å2
Baniso -1Baniso -2Baniso -3
1--2.415 Å2-0 Å20 Å2
2--3.498 Å2-0 Å2
3----1.083 Å2
Refinement stepCycle: LAST / Resolution: 1.5→30.994 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 37 58 1203
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0121206
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161144
X-RAY DIFFRACTIONr_angle_refined_deg1.6531.851647
X-RAY DIFFRACTIONr_angle_other_deg0.5851.7632634
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.7375144
X-RAY DIFFRACTIONr_dihedral_angle_2_deg5.55259
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.28410196
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.571057
X-RAY DIFFRACTIONr_chiral_restr0.0790.2175
X-RAY DIFFRACTIONr_chiral_restr_other1.6850.28
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.021428
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02286
X-RAY DIFFRACTIONr_nbd_refined0.1950.2148
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1950.21005
X-RAY DIFFRACTIONr_nbtor_refined0.1660.2559
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.2631
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1340.245
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1660.211
X-RAY DIFFRACTIONr_nbd_other0.1870.251
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1320.27
X-RAY DIFFRACTIONr_mcbond_it7.2222.393570
X-RAY DIFFRACTIONr_mcbond_other7.2032.392570
X-RAY DIFFRACTIONr_mcangle_it9.3554.317716
X-RAY DIFFRACTIONr_mcangle_other9.3564.319717
X-RAY DIFFRACTIONr_scbond_it9.3852.791636
X-RAY DIFFRACTIONr_scbond_other9.3782.791637
X-RAY DIFFRACTIONr_scangle_it12.9314.97931
X-RAY DIFFRACTIONr_scangle_other12.9244.969932
X-RAY DIFFRACTIONr_lrange_it15.73627.1991206
X-RAY DIFFRACTIONr_lrange_other15.58726.7061200
X-RAY DIFFRACTIONr_rigid_bond_restr4.2332350
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
1.5-1.5390.325740.29913680.314440.9190.94999.86150.292
1.539-1.5810.35920.31413520.31714440.9280.9421000.3
1.581-1.6270.342750.28213340.28614090.9410.9511000.266
1.627-1.6770.256630.25712780.25713410.9310.9691000.229
1.677-1.7310.249620.24312660.24413280.960.9721000.213
1.731-1.7920.323680.19212040.19912720.9380.9821000.16
1.792-1.8590.217560.16311860.16512420.9820.9891000.125
1.859-1.9350.239630.14111260.14611900.9790.99199.9160.112
1.935-2.0210.181550.13910980.14111530.9820.9921000.112
2.021-2.1190.248650.14910160.15410830.960.98999.81530.122
2.119-2.2330.229630.1489910.15310540.9690.9881000.127
2.233-2.3680.288520.1399370.1459890.9470.9891000.123
2.368-2.530.282580.1468780.1539370.9590.9999.89330.131
2.53-2.7310.205350.1538510.1558880.9770.98899.77480.14
2.731-2.990.246280.1717760.1748040.9610.9821000.166
2.99-3.3390.139330.1547100.1537430.9860.9841000.159
3.339-3.8480.207470.1446180.1496660.9740.98799.84990.154
3.848-4.6940.102220.1375440.1355690.9930.98899.47280.156
4.694-6.5640.198160.1594440.1614600.9660.9861000.197
6.564-30.9940.269110.2192790.2212900.9660.9731000.249

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