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- PDB-6rzm: Galectin-3C in complex with trifluoroaryltriazole monothiogalacto... -

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Basic information

Entry
Database: PDB / ID: 6rzm
TitleGalectin-3C in complex with trifluoroaryltriazole monothiogalactoside derivative:5(Iodine)
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 NK T cell activation / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / 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 / 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 / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / signaling receptor inhibitor activity / 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 / immunological synapse / ficolin-1-rich granule membrane / laminin binding / neutrophil chemotaxis / epithelial cell differentiation / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-KON / DI(HYDROXYETHYL)ETHER / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.345 Å
AuthorsKumar, R. / Verteramo, M.L. / Nilsson, U.J. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Knut and Alice Wallenberg FoundationKAW 2013.0022 Sweden
CitationJournal: to be published
Title: Thermodynamic studies of halogen-bond interactions in galectin-3
Authors: Verteramo, M.L. / Zetterberg, F. / Kumar, R. / Wallerstein, J. / Ignjatovic, M.M. / Leffler, H. / Ryde, U. / Logan, D.T. / Akke, M. / Nilsson, U.J.
History
DepositionJun 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 8, 2020Provider: repository / Type: Initial release
Revision 1.1Jan 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 / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_diffrn_id

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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)16,4224
Polymers15,7011
Non-polymers7213
Water2,702150
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area410 Å2
ΔGint-6 kcal/mol
Surface area7140 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.070, 57.238, 61.655
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 BL21(DE3) (bacteria) / References: UniProt: P17931
#2: Chemical ChemComp-KON / (2~{R},3~{R},4~{S},5~{R},6~{R})-2-(hydroxymethyl)-6-(3-iodanylphenyl)sulfanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxane-3,5-diol


Mass: 579.331 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H17F3IN3O4S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#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.: 150 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.03 Å3/Da / Density % sol: 39.31 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% PEG 4000, 0.1 M Tris/HCl pH 7.5, 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 IV / Beamline: BioMAX / Wavelength: 0.652 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Jan 24, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.652 Å / Relative weight: 1
ReflectionResolution: 1.34→28.62 Å / Num. obs: 29030 / % possible obs: 99.61 % / Redundancy: 13.2 % / Net I/σ(I): 9.88
Reflection shellResolution: 1.34→1.39 Å / Num. unique obs: 2836

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Processing

Software
NameVersionClassification
PHENIX(1.14_3260: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSL

3zsl


Resolution: 1.345→28.619 Å / SU ML: 0.2 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 21.36 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.188 1439 4.97 %
Rwork0.1525 --
obs0.1543 28937 99.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.345→28.619 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 40 150 1296
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051263
X-RAY DIFFRACTIONf_angle_d0.8711738
X-RAY DIFFRACTIONf_dihedral_angle_d13.032516
X-RAY DIFFRACTIONf_chiral_restr0.085195
X-RAY DIFFRACTIONf_plane_restr0.006228
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.3453-1.39340.38261330.34912618X-RAY DIFFRACTION96
1.3934-1.44910.28791670.27212701X-RAY DIFFRACTION100
1.4491-1.51510.32591290.22892720X-RAY DIFFRACTION100
1.5151-1.5950.2761480.18692714X-RAY DIFFRACTION100
1.595-1.69490.2261510.15232736X-RAY DIFFRACTION100
1.6949-1.82570.1891570.14052724X-RAY DIFFRACTION100
1.8257-2.00940.19961370.10952760X-RAY DIFFRACTION100
2.0094-2.30010.16721270.11062783X-RAY DIFFRACTION100
2.3001-2.89740.16191230.13892817X-RAY DIFFRACTION100
2.8974-28.62550.1621670.15782925X-RAY DIFFRACTION100

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