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

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Basic information

Entry
Database: PDB / ID: 6qlr
TitleGalectin-3C in complex with fluoroaryltriazole 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 protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / 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 / positive chemotaxis / macrophage chemotaxis / regulation of T cell proliferation / 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 / molecular condensate scaffold activity / neutrophil chemotaxis / RNA splicing / secretory granule membrane / positive regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / mRNA processing / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / 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-J4N / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 0.97 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

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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
Water4,756264
1


  • Idetical with deposited unit
  • defined by 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)36.778, 57.822, 62.707
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-J4N / (2~{R},3~{R},4~{S},5~{R},6~{S})-4-[4-[3,5-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 / Chloride


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


Mass: 18.015 Da / Num. of mol.: 264 / 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: 2.15 Å3/Da / Density % sol: 42.8 %
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 II / Beamline: I911-3 / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: May 4, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 0.97→31.354 Å / Num. obs: 78756 / % possible obs: 98.44 % / Redundancy: 4.3 % / CC1/2: 0.999 / Rmerge(I) obs: 0.05891 / Rpim(I) all: 0.03183 / Rrim(I) all: 0.06727 / Net I/σ(I): 13.8
Reflection shellResolution: 0.97→1.005 Å / Rmerge(I) obs: 1.421 / Num. unique obs: 7095 / Rpim(I) all: 0.8843 / Rrim(I) all: 1.688 / % possible all: 88.03

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Processing

Software
NameVersionClassification
PHENIX(dev_3084: ???)refinement
XDSdata reduction
Aimlessdata scaling
PHENIXphasing
RefinementResolution: 0.97→31.354 Å / SU ML: 0.11 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 15.74
RfactorNum. reflection% reflection
Rfree0.1561 3933 5.01 %
Rwork0.1375 --
obs0.1384 78560 98.44 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 0.97→31.354 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 32 264 1402
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.011247
X-RAY DIFFRACTIONf_angle_d1.1311714
X-RAY DIFFRACTIONf_dihedral_angle_d15.348485
X-RAY DIFFRACTIONf_chiral_restr0.111191
X-RAY DIFFRACTIONf_plane_restr0.008226
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
0.97-0.98180.5412990.48322018X-RAY DIFFRACTION76
0.9818-0.99430.32551200.35642494X-RAY DIFFRACTION92
0.9943-1.00740.33211300.30492614X-RAY DIFFRACTION99
1.0074-1.02120.25851310.27672660X-RAY DIFFRACTION99
1.0212-1.03570.24861330.23462651X-RAY DIFFRACTION100
1.0357-1.05120.25541400.22252707X-RAY DIFFRACTION99
1.0512-1.06760.19681450.20012626X-RAY DIFFRACTION100
1.0676-1.08510.18851540.18452665X-RAY DIFFRACTION99
1.0851-1.10380.16971440.16142662X-RAY DIFFRACTION100
1.1038-1.12390.15991470.14382665X-RAY DIFFRACTION100
1.1239-1.14550.16011320.14182662X-RAY DIFFRACTION100
1.1455-1.16890.13761460.13442687X-RAY DIFFRACTION100
1.1689-1.19430.16181220.12352707X-RAY DIFFRACTION100
1.1943-1.22210.14891270.11782735X-RAY DIFFRACTION100
1.2221-1.25270.14121460.11342654X-RAY DIFFRACTION100
1.2527-1.28660.12611530.1122673X-RAY DIFFRACTION100
1.2866-1.32440.14051490.10972703X-RAY DIFFRACTION100
1.3244-1.36720.12771450.10942701X-RAY DIFFRACTION100
1.3672-1.4160.14091290.11022699X-RAY DIFFRACTION100
1.416-1.47270.11961470.10242703X-RAY DIFFRACTION100
1.4727-1.53980.1211400.10382710X-RAY DIFFRACTION100
1.5398-1.62090.13371400.10752707X-RAY DIFFRACTION100
1.6209-1.72250.14341750.10792699X-RAY DIFFRACTION100
1.7225-1.85550.1321600.11932725X-RAY DIFFRACTION100
1.8555-2.04210.1171550.11042713X-RAY DIFFRACTION100
2.0421-2.33760.13981290.1192765X-RAY DIFFRACTION100
2.3376-2.94470.13811290.14252802X-RAY DIFFRACTION100
2.9447-31.36990.17641660.14222820X-RAY DIFFRACTION97

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