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- PDB-8pff: Galectin-3C in complex with a triazolesulfone derivative -

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Basic information

Entry
Database: PDB / ID: 8pff
TitleGalectin-3C in complex with a triazolesulfone derivative
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / INHIBITOR / COMPLEX / STRUCTURE-BASED INHIBITOR DESIGN
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / 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 / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / 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 / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / 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 / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / neutrophil chemotaxis / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / 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 / cytoplasm / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
THIOCYANATE ION / Chem-YJF / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.08 Å
AuthorsKumar, R. / Mahanti, M. / Nilsson, U.J. / Logan, D.T.
Funding support Sweden, 4items
OrganizationGrant numberCountry
Swedish Research Council2016-04855 Sweden
Swedish Research Council2016-036767 Sweden
Swedish Research Council2020-03317 Sweden
The Crafoord Foundation20190803 Sweden
Citation
Journal: J.Med.Chem. / Year: 2023
Title: Ligand Sulfur Oxidation State Progressively Alters Galectin-3-Ligand Complex Conformations To Induce Affinity-Influencing Hydrogen Bonds.
Authors: Mahanti, M. / Pal, K.B. / Kumar, R. / Schulze, M. / Leffler, H. / Logan, D.T. / Nilsson, U.J.
#1: Journal: Acta Crystallogr D Struct Biol / Year: 2019
Title: Macromolecular structure determination using X-rays, neutrons and electrons: recent developments in Phenix.
Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty ...Authors: Dorothee Liebschner / Pavel V Afonine / Matthew L Baker / Gábor Bunkóczi / Vincent B Chen / Tristan I Croll / Bradley Hintze / Li Wei Hung / Swati Jain / Airlie J McCoy / Nigel W Moriarty / Robert D Oeffner / Billy K Poon / Michael G Prisant / Randy J Read / Jane S Richardson / David C Richardson / Massimo D Sammito / Oleg V Sobolev / Duncan H Stockwell / Thomas C Terwilliger / Alexandre G Urzhumtsev / Lizbeth L Videau / Christopher J Williams / Paul D Adams /
Abstract: Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological ...Diffraction (X-ray, neutron and electron) and electron cryo-microscopy are powerful methods to determine three-dimensional macromolecular structures, which are required to understand biological processes and to develop new therapeutics against diseases. The overall structure-solution workflow is similar for these techniques, but nuances exist because the properties of the reduced experimental data are different. Software tools for structure determination should therefore be tailored for each method. Phenix is a comprehensive software package for macromolecular structure determination that handles data from any of these techniques. Tasks performed with Phenix include data-quality assessment, map improvement, model building, the validation/rebuilding/refinement cycle and deposition. Each tool caters to the type of experimental data. The design of Phenix emphasizes the automation of procedures, where possible, to minimize repetitive and time-consuming manual tasks, while default parameters are chosen to encourage best practice. A graphical user interface provides access to many command-line features of Phenix and streamlines the transition between programs, project tracking and re-running of previous tasks.
History
DepositionJun 15, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 8, 2023Provider: repository / Type: Initial release
Revision 1.1Nov 22, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID

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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)16,3334
Polymers15,7011
Non-polymers6323
Water2,882160
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)33.990, 57.777, 61.579
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Space group name HallP2ac2ab
Symmetry operation#1: x,y,z
#2: x+1/2,-y+1/2,-z
#3: -x,y+1/2,-z+1/2
#4: -x+1/2,-y,z+1/2

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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) / References: UniProt: P17931
#2: Chemical ChemComp-SCN / THIOCYANATE ION


Mass: 58.082 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CNS
#3: Chemical ChemComp-YJF / (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-(phenylsulfonyl)-1,2,3-triazol-1-yl]oxan-2-yl]sulfanyl-oxane-3,4,5-triol


Mass: 549.572 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H27N3O11S2 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 160 / 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: 1.93 Å3/Da / Density % sol: 36.12 %
Crystal growTemperature: 295 K / Method: vapor diffusion, hanging drop / pH: 7.5 / Details: 20% (w/v) PEG 4000, Tris-HCl pH 7.5, 0.4 M NaSCN / Temp details: room temperature

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.7749 Å
DetectorType: DECTRIS EIGER X 16M / Detector: PIXEL / Date: Mar 23, 2018
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.7749 Å / Relative weight: 1
ReflectionResolution: 1.08→29.3 Å / Num. obs: 51395 / % possible obs: 97.6 % / Redundancy: 12.5 % / Biso Wilson estimate: 10.99 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.124 / Net I/σ(I): 8.92
Reflection shellResolution: 1.08→1.12 Å / Rmerge(I) obs: 1.622 / Mean I/σ(I) obs: 0.85 / Num. unique obs: 4240 / CC1/2: 0.376 / % possible all: 75.8

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Processing

Software
NameVersionClassification
PHENIX1.21rc1_4933refinement
XDS20180409data reduction
XSCALE20180409data scaling
PHENIX1.21rc1_4933phasing
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.08→29.3 Å / SU ML: 0.1772 / Cross valid method: FREE R-VALUE / σ(F): 1.33 / Phase error: 24.7599
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2028 2466 4.83 %
Rwork0.1783 48561 -
obs0.1796 51027 97.62 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 15.83 Å2
Refinement stepCycle: LAST / Resolution: 1.08→29.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 40 160 1303
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.02111215
X-RAY DIFFRACTIONf_angle_d1.70051663
X-RAY DIFFRACTIONf_chiral_restr0.1261189
X-RAY DIFFRACTIONf_plane_restr0.0254216
X-RAY DIFFRACTIONf_dihedral_angle_d8.5541166
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.08-1.10.661840.59391530X-RAY DIFFRACTION56.67
1.1-1.130.29321160.30112747X-RAY DIFFRACTION99.97
1.13-1.150.27871340.24292727X-RAY DIFFRACTION99.97
1.15-1.180.26951630.21182709X-RAY DIFFRACTION100
1.18-1.210.26251350.21322733X-RAY DIFFRACTION100
1.21-1.240.28341140.19822749X-RAY DIFFRACTION100
1.24-1.280.241530.18982718X-RAY DIFFRACTION100
1.28-1.320.22431340.18182741X-RAY DIFFRACTION100
1.32-1.370.22811380.18472745X-RAY DIFFRACTION99.97
1.37-1.420.20481230.17512767X-RAY DIFFRACTION100
1.42-1.480.19281380.15922751X-RAY DIFFRACTION100
1.48-1.560.17781490.14652754X-RAY DIFFRACTION100
1.56-1.660.21891360.1442754X-RAY DIFFRACTION100
1.66-1.790.18811640.15112752X-RAY DIFFRACTION100
1.79-1.970.20381210.15042806X-RAY DIFFRACTION99.97
1.97-2.250.20061480.1532797X-RAY DIFFRACTION99.97
2.25-2.840.18761350.17612848X-RAY DIFFRACTION99.93
2.84-29.30.16421810.17472933X-RAY DIFFRACTION99.87

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