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- PDB-5oax: Galectin-3c in complex with thiogalactoside derivate -

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Basic information

Entry
Database: PDB / ID: 5oax
TitleGalectin-3c in complex with thiogalactoside derivate
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


: / 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 / mononuclear cell migration / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding ...: / 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 / mononuclear cell migration / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / protein phosphatase inhibitor activity / negative regulation of T cell receptor signaling pathway / regulation of T cell proliferation / positive chemotaxis / macrophage chemotaxis / positive regulation of calcium ion import / chemoattractant activity / monocyte chemotaxis / 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 / molecular condensate scaffold activity / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / RNA binding / extracellular space / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-9Q5 / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.2 Å
AuthorsNilsson, U.J. / Peterson, K. / Hakansson, M. / Logan, D.T.
CitationJournal: J. Med. Chem. / Year: 2018
Title: Systematic Tuning of Fluoro-galectin-3 Interactions Provides Thiodigalactoside Derivatives with Single-Digit nM Affinity and High Selectivity.
Authors: Peterson, K. / Kumar, R. / Stenstrom, O. / Verma, P. / Verma, P.R. / Hakansson, M. / Kahl-Knutsson, B. / Zetterberg, F. / Leffler, H. / Akke, M. / Logan, D.T. / Nilsson, U.J.
History
DepositionJun 25, 2017Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 2, 2018Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2019Group: Data collection / Category: reflns_shell
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,4332
Polymers15,7351
Non-polymers6981
Water4,125229
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: native gel electrophoresis
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7520 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.190, 58.150, 62.810
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: 15735.129 Da / Num. of mol.: 1 / Fragment: UNP residues 114-250
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-9Q5 / 5,6-bis(fluoranyl)-3-[[(2~{S},3~{R},4~{S},5~{S},6~{R})-2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-4-yl]oxymethyl]chromen-2-one


Mass: 697.633 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C30H30F3N3O11S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 229 / Source method: isolated from a natural source / Formula: H2O

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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: 2.1 Å3/Da / Density % sol: 41.43 %
Crystal growTemperature: 298 K / Method: vapor diffusion
Details: 19.2 mg/mL GALECTIN-3C, 100mM NaCl, 0.1 M TRIS/HCL, pH 7.5, 30 % PEG 4000, 0.4 M NaSCN, 0.1M MgCl2, 10 mM BETA-MERCAPTOETHANOL, 4.9 mM INHIBITOR COMPOUND

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Aug 12, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→30 Å / Num. obs: 42317 / % possible obs: 99.7 % / Redundancy: 5.5 % / Biso Wilson estimate: 9.2 Å2 / Rmerge(I) obs: 0.057 / Net I/σ(I): 19.3

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Processing

SoftwareName: REFMAC / Version: 5.8.0158 / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.2→29.07 Å / Cor.coef. Fo:Fc: 0.985 / Cor.coef. Fo:Fc free: 0.979 / SU B: 1.086 / SU ML: 0.022 / Cross valid method: THROUGHOUT / ESU R: 0.032 / ESU R Free: 0.033 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13195 2116 5 %RANDOM
Rwork0.10264 ---
obs0.10412 40200 99.78 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 12.979 Å2
Baniso -1Baniso -2Baniso -3
1--0.23 Å20 Å20 Å2
2--0.39 Å20 Å2
3----0.16 Å2
Refinement stepCycle: 1 / Resolution: 1.2→29.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 48 229 1383
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.0191472
X-RAY DIFFRACTIONr_bond_other_d0.0030.021371
X-RAY DIFFRACTIONr_angle_refined_deg2.5222.0362047
X-RAY DIFFRACTIONr_angle_other_deg1.31833229
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8225192
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.83323.7572
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.07315261
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.6411514
X-RAY DIFFRACTIONr_chiral_restr0.1520.2229
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0211627
X-RAY DIFFRACTIONr_gen_planes_other0.0070.02301
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_it1.4290.902634
X-RAY DIFFRACTIONr_mcbond_other1.4310.899633
X-RAY DIFFRACTIONr_mcangle_it1.8591.362810
X-RAY DIFFRACTIONr_mcangle_other1.8591.363811
X-RAY DIFFRACTIONr_scbond_it3.2161.266838
X-RAY DIFFRACTIONr_scbond_other3.2051.261832
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other3.3271.8271211
X-RAY DIFFRACTIONr_long_range_B_refined13.47113.7951620
X-RAY DIFFRACTIONr_long_range_B_other13.47913.7881618
X-RAY DIFFRACTIONr_rigid_bond_restr5.37632843
X-RAY DIFFRACTIONr_sphericity_free44.7965150
X-RAY DIFFRACTIONr_sphericity_bonded17.3852863
LS refinement shellResolution: 1.198→1.229 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.194 150 -
Rwork0.163 2864 -
obs--97.57 %

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