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- PDB-6qls: Galectin-3C in complex with fluoroaryltriazole monothiogalactosid... -

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Basic information

Entry
Database: PDB / ID: 6qls
TitleGalectin-3C in complex with fluoroaryltriazole monothiogalactoside derivative 6
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 / 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 / chemoattractant activity / positive regulation of calcium ion import / 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 / positive regulation of protein-containing complex assembly / spliceosomal complex / molecular condensate scaffold activity / mRNA processing / carbohydrate binding / protein phosphatase binding / collagen-containing extracellular matrix / 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-HRK / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.047 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: Chemmedchem / Year: 2019
Title: Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions.
Authors: Kumar, R. / Ignjatovic, M.M. / Peterson, K. / Olsson, M. / Leffler, H. / Ryde, U. / Nilsson, U.J. / Logan, D.T.
History
DepositionFeb 1, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 10, 2019Provider: repository / Type: Initial release
Revision 1.1Aug 28, 2019Group: Data collection / Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.title
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)16,2223
Polymers15,7011
Non-polymers5212
Water5,044280
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area7510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.481, 58.600, 63.128
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-HRK / (2~{R},3~{S},4~{S},5~{R},6~{S})-2-(hydroxymethyl)-6-[(2~{S},3~{R},4~{S},5~{R},6~{R})-6-(hydroxymethyl)-3,5-bis(oxidanyl)-4-(4-phenyl-1,2,3-triazol-1-yl)oxan-2-yl]sulfanyl-oxane-3,4,5-triol


Mass: 485.508 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O9S / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 280 / 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: 2.17 Å3/Da / Density % sol: 43.4 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
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 IV / Beamline: BioMAX / Wavelength: 0.635784 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: May 30, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.635784 Å / Relative weight: 1
ReflectionResolution: 1.047→22.844 Å / Num. obs: 64101 / % possible obs: 99.38 % / Redundancy: 6.6 % / CC1/2: 0.999 / Rmerge(I) obs: 0.09139 / Rpim(I) all: 0.03844 / Rrim(I) all: 0.09932 / Net I/σ(I): 8.98
Reflection shellResolution: 1.047→1.085 Å / Rmerge(I) obs: 1.218 / Mean I/σ(I) obs: 0.89 / Num. unique obs: 6158 / CC1/2: 0.475 / Rpim(I) all: 0.5114 / % possible all: 96.28

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Processing

Software
NameVersionClassification
PHENIX(dev_3084: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3zsl

3zsl


Resolution: 1.047→22.844 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.81
RfactorNum. reflection% reflection
Rfree0.1599 3304 5.16 %
Rwork0.1363 --
obs0.1375 63982 99.2 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.047→22.844 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1105 0 34 280 1419
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0121284
X-RAY DIFFRACTIONf_angle_d1.3361765
X-RAY DIFFRACTIONf_dihedral_angle_d12.45502
X-RAY DIFFRACTIONf_chiral_restr0.106200
X-RAY DIFFRACTIONf_plane_restr0.009231
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.0466-1.06160.2951030.29932213X-RAY DIFFRACTION87
1.0616-1.07740.28451300.25362493X-RAY DIFFRACTION100
1.0774-1.09430.24961540.22792464X-RAY DIFFRACTION100
1.0943-1.11220.22041560.20772498X-RAY DIFFRACTION100
1.1122-1.13140.21821270.19412519X-RAY DIFFRACTION100
1.1314-1.1520.21371370.18662521X-RAY DIFFRACTION100
1.152-1.17410.2161460.1762500X-RAY DIFFRACTION100
1.1741-1.19810.18371200.16692527X-RAY DIFFRACTION100
1.1981-1.22410.18921390.16192505X-RAY DIFFRACTION100
1.2241-1.25260.19071490.15932531X-RAY DIFFRACTION99
1.2526-1.28390.17381270.14942514X-RAY DIFFRACTION100
1.2839-1.31860.17841550.14732494X-RAY DIFFRACTION100
1.3186-1.35740.18441540.15092516X-RAY DIFFRACTION100
1.3574-1.40120.1741560.14392516X-RAY DIFFRACTION100
1.4012-1.45130.1591310.13282526X-RAY DIFFRACTION100
1.4513-1.50940.16811310.12162553X-RAY DIFFRACTION100
1.5094-1.57810.16811250.11372546X-RAY DIFFRACTION100
1.5781-1.66130.14611520.11442553X-RAY DIFFRACTION100
1.6613-1.76530.15891390.11372551X-RAY DIFFRACTION100
1.7653-1.90150.13531410.11222550X-RAY DIFFRACTION100
1.9015-2.09280.13711320.11092597X-RAY DIFFRACTION100
2.0928-2.39530.14671540.11772571X-RAY DIFFRACTION100
2.3953-3.01680.15551190.13682660X-RAY DIFFRACTION100
3.0168-22.84970.12791270.13222760X-RAY DIFFRACTION100

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