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- PDB-6qlo: Galectin-3C in complex with substituted fluoroaryltriazole monoth... -

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Basic information

Entry
Database: PDB / ID: 6qlo
TitleGalectin-3C in complex with substituted fluoroaryltriazole monothiogalactoside derivative 1
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 / cytoplasm / cytosol
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-J5E / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.18 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)16,1863
Polymers15,7011
Non-polymers4852
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area7280 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.392, 57.790, 62.858
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-J5E / (2~{R},3~{R},4~{S},5~{R},6~{S})-4-[4-[3,4-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-(hydroxymethyl)-6-(4-methylphenyl)sulfanyl-oxane-3,5-diol


Mass: 449.471 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H21F2N3O4S / 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.: 181 / 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: 2.13 Å3/Da / Density % sol: 42.3 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 20% 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: May 3, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.18→42.55 Å / Num. obs: 42509 / % possible obs: 95.85 % / Redundancy: 6.1 % / Biso Wilson estimate: 10.27 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.05072 / Rpim(I) all: 0.02225 / Rrim(I) all: 0.05551 / Net I/σ(I): 21.37
Reflection shellResolution: 1.18→1.222 Å / Redundancy: 5.6 % / Rmerge(I) obs: 0.848 / Mean I/σ(I) obs: 2.17 / Num. unique obs: 4033 / CC1/2: 0.768 / Rpim(I) all: 0.3836 / Rrim(I) all: 0.9333 / % possible all: 92.12

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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: 1.18→42.55 Å / SU ML: 0.1 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 14.97
RfactorNum. reflection% reflection
Rfree0.1535 2137 5.03 %
Rwork0.1326 --
obs0.1336 42509 95.85 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.18→42.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 32 181 1319
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0111228
X-RAY DIFFRACTIONf_angle_d1.1351683
X-RAY DIFFRACTIONf_dihedral_angle_d16.233472
X-RAY DIFFRACTIONf_chiral_restr0.104187
X-RAY DIFFRACTIONf_plane_restr0.007221
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.18-1.20750.28181250.22832536X-RAY DIFFRACTION91
1.2075-1.23770.20061290.19332593X-RAY DIFFRACTION94
1.2377-1.27110.18481140.16972627X-RAY DIFFRACTION94
1.2711-1.30850.20791290.16022618X-RAY DIFFRACTION94
1.3085-1.35080.16731400.15152619X-RAY DIFFRACTION95
1.3508-1.3990.20211430.1442658X-RAY DIFFRACTION95
1.399-1.45510.16681460.12242651X-RAY DIFFRACTION95
1.4551-1.52130.1651600.1132654X-RAY DIFFRACTION96
1.5213-1.60150.15851530.10382655X-RAY DIFFRACTION96
1.6015-1.70180.15751480.10282710X-RAY DIFFRACTION97
1.7018-1.83320.14821620.10362699X-RAY DIFFRACTION97
1.8332-2.01770.13161290.10462785X-RAY DIFFRACTION97
2.0177-2.30950.13661230.11342799X-RAY DIFFRACTION98
2.3095-2.90940.15761680.13722807X-RAY DIFFRACTION99
2.9094-31.50570.13281680.14922961X-RAY DIFFRACTION99

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