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- PDB-6i78: Galectin-3C in complex with substituted polyfluoroaryl monothioga... -

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Basic information

Entry
Database: PDB / ID: 6i78
TitleGalectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative 5
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE-BINDING PROTEIN / GALACTOSE-SPECIFIC LECTIN 3 / GALACTOSIDE-BINDING PROTEIN / GALBP / IGE-6 BINDING PROTEIN / L-31 / LAMININ-BINDING PROTEIN / LECTIN L-29 / MAC-2
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-H5H / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.15 Å
AuthorsKumar, R. / Peterson, K. / Nilsson, U.J. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2013.0022 Sweden
CitationJournal: Org. Biomol. Chem. / Year: 2019
Title: Substituted polyfluoroaryl interactions with an arginine side chain in galectin-3 are governed by steric-, desolvation and electronic conjugation effects.
Authors: Kumar, R. / Peterson, K. / Misini Ignjatovic, M. / Leffler, H. / Ryde, U. / Nilsson, U.J. / Logan, D.T.
History
DepositionNov 15, 2018Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 23, 2019Provider: repository / Type: Initial release
Revision 1.1Feb 13, 2019Group: Data collection / Database references / Category: citation / citation_author / pdbx_database_proc
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.2Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,2162
Polymers15,7011
Non-polymers5141
Water3,027168
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.307, 57.628, 62.913
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: 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) / Strain (production host): BL21(DE3) / References: UniProt: P17931
#2: Chemical ChemComp-H5H / (2~{R},3~{R},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-4-[4-[2,3,5,6-tetrakis(fluoranyl)-4-(methylamino)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 514.493 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H22F4N4O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 168 / 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: 2.12 Å3/Da / Density % sol: 42 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 30% PEG 4000, 0.1 M Tris/HCl pH 7.5, 0.1 M MgCl2, 0.4 M NaSCN, 7.9 mM beta-mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Oct 17, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.15→31.446 Å / Num. obs: 45668 / % possible obs: 95.78 % / Redundancy: 14.96 % / Biso Wilson estimate: 9.75 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.04181 / Rpim(I) all: 0.03001 / Net I/av σ(I): 14.96 / Net I/σ(I): 14.96
Reflection shellResolution: 1.15→1.19 Å / Rmerge(I) obs: 0.5445 / Mean I/σ(I) obs: 1.39 / CC1/2: 0.706 / Rpim(I) all: 0.4352 / % possible all: 89.19

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Processing

Software
NameVersionClassification
PHENIX(dev_3084: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 3ZSL

3zsl


Resolution: 1.15→31.446 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 16.39 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.1679 2309 5.06 %
Rwork0.138 --
obs0.1395 45664 95.78 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.15→31.446 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 35 168 1309
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0161251
X-RAY DIFFRACTIONf_angle_d1.371717
X-RAY DIFFRACTIONf_dihedral_angle_d16.778506
X-RAY DIFFRACTIONf_chiral_restr0.117189
X-RAY DIFFRACTIONf_plane_restr0.009250
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.1501-1.17510.27931210.29052380X-RAY DIFFRACTION84
1.1751-1.20240.28231540.25242731X-RAY DIFFRACTION98
1.2024-1.23250.26151500.2132738X-RAY DIFFRACTION99
1.2325-1.26580.21681300.18772731X-RAY DIFFRACTION98
1.2658-1.3030.20731370.16822722X-RAY DIFFRACTION97
1.303-1.34510.20371420.15712706X-RAY DIFFRACTION96
1.3451-1.39320.19361580.15122661X-RAY DIFFRACTION96
1.3932-1.4490.1911600.13522689X-RAY DIFFRACTION96
1.449-1.51490.18111510.1142684X-RAY DIFFRACTION96
1.5149-1.59480.14321460.09982686X-RAY DIFFRACTION96
1.5948-1.69470.13151460.09472720X-RAY DIFFRACTION97
1.6947-1.82550.14441070.0992805X-RAY DIFFRACTION97
1.8255-2.00920.1521610.10022769X-RAY DIFFRACTION98
2.0092-2.29980.13521490.10822778X-RAY DIFFRACTION97
2.2998-2.89720.15851330.14222788X-RAY DIFFRACTION96
2.8972-31.4580.15761640.15012767X-RAY DIFFRACTION92

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