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

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Basic information

Entry
Database: PDB / ID: 8rrb
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: 1.2 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)16,8545
Polymers15,7011
Non-polymers1,1534
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1730 Å2
ΔGint-2 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.490, 56.900, 61.070
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-A1H2P / ~{N}-~{tert}-butyl-4-[4-[[(2~{R},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3-methoxy-5-oxidanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-2-yl]methyl]-1,2,3-triazol-1-yl]piperidine-1-carboxamide


Mass: 622.639 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H37F3N8O5 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-2PE / NONAETHYLENE GLYCOL


Mass: 414.488 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C18H38O10 / Comment: precipitant*YM
#4: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CNS
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.1 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: Aug 21, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1→41.63 Å / Num. obs: 68875 / % possible obs: 99.3 % / Redundancy: 5.95 % / CC1/2: 0.999 / Rrim(I) all: 0.057 / Net I/σ(I): 14.49
Reflection shellResolution: 1→1.06 Å / Mean I/σ(I) obs: 1.25 / Num. unique obs: 10629 / CC1/2: 0.532 / Rrim(I) all: 1.114 / % possible all: 96.1

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
autoPROCdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→41.603 Å / Cor.coef. Fo:Fc: 0.969 / Cor.coef. Fo:Fc free: 0.966 / SU B: 1.392 / SU ML: 0.028 / Cross valid method: FREE R-VALUE / ESU R: 0.046 / ESU R Free: 0.041
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1771 2026 5.002 %
Rwork0.1611 38480 -
all0.162 --
obs-40506 99.931 %
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: 10.347 Å2
Baniso -1Baniso -2Baniso -3
1--0.753 Å2-0 Å2-0 Å2
2---1.447 Å20 Å2
3---2.2 Å2
Refinement stepCycle: LAST / Resolution: 1.2→41.603 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1107 0 62 157 1326
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0040.0121298
X-RAY DIFFRACTIONr_bond_other_d0.0010.0161224
X-RAY DIFFRACTIONr_angle_refined_deg1.221.8521777
X-RAY DIFFRACTIONr_angle_other_deg0.4491.7612819
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8545158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg3.34510
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.59310204
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.7381063
X-RAY DIFFRACTIONr_chiral_restr0.0610.2183
X-RAY DIFFRACTIONr_chiral_restr_other0.0210.26
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021575
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02313
X-RAY DIFFRACTIONr_nbd_refined0.2060.2167
X-RAY DIFFRACTIONr_symmetry_nbd_other0.1990.21055
X-RAY DIFFRACTIONr_nbtor_refined0.1650.2571
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0820.2635
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1280.291
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.1270.27
X-RAY DIFFRACTIONr_nbd_other0.1710.240
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.110.217
X-RAY DIFFRACTIONr_mcbond_it1.3350.999607
X-RAY DIFFRACTIONr_mcbond_other1.3230.996605
X-RAY DIFFRACTIONr_mcangle_it2.0831.792772
X-RAY DIFFRACTIONr_mcangle_other2.0841.793773
X-RAY DIFFRACTIONr_scbond_it1.8491.148691
X-RAY DIFFRACTIONr_scbond_other1.8431.148690
X-RAY DIFFRACTIONr_scangle_it2.8852.0461005
X-RAY DIFFRACTIONr_scangle_other2.8762.0441004
X-RAY DIFFRACTIONr_lrange_it8.1213.1721328
X-RAY DIFFRACTIONr_lrange_other8.1313.1761329
X-RAY DIFFRACTIONr_rigid_bond_restr1.33332522
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
1.2-1.2310.1941480.18728100.18829590.9810.9899.96620.159
1.231-1.2650.2081440.18127480.18228930.9750.98199.96540.152
1.265-1.3010.1731410.16626670.16628100.9810.98499.92880.139
1.301-1.3410.1571340.1625580.1626930.9840.98699.96290.135
1.341-1.3850.1891330.16325130.16526460.9810.9851000.137
1.385-1.4340.161270.16124120.16125390.9790.9861000.136
1.434-1.4880.1861240.14823560.14924800.9860.9881000.124
1.488-1.5490.1811180.14622580.14723770.9820.98999.95790.127
1.549-1.6180.1621150.14721770.14822920.9830.9881000.128
1.618-1.6960.1891100.14520820.14821920.980.9881000.129
1.696-1.7880.1411050.14719980.14721040.9870.98799.95250.134
1.788-1.8960.158980.14518710.14619690.9860.9881000.138
1.896-2.0270.157940.13917910.1418870.9820.98999.8940.139
2.027-2.1890.16870.14416440.14517330.9870.98999.88460.148
2.189-2.3970.173800.14815300.14916100.9810.9861000.157
2.397-2.6790.183740.17413910.17414680.980.98299.79560.185
2.679-3.0910.18660.16912510.16913190.980.98299.84840.189
3.091-3.7810.195560.1710650.17111220.9780.98299.91090.198
3.781-5.3250.163440.1618420.1618880.9830.98499.77480.194
5.325-41.6030.246270.2485050.2485400.9770.95498.51850.304

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