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- PDB-6q17: Crystal structure of Human galectin-3 CRD in complex with Methyl ... -

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Basic information

Entry
Database: PDB / ID: 6q17
TitleCrystal structure of Human galectin-3 CRD in complex with Methyl 3-O-[1-(b-D-galactopyranosyl)-1,2,3-triazol-4-yl]-methyl-b-D-galactopyranoside
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN
Function / homology
Function and homology information


negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / 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 / disaccharide binding / 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 / 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 / disaccharide binding / 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 / positive chemotaxis / regulation of T cell proliferation / positive regulation of calcium ion import / macrophage chemotaxis / chemoattractant activity / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / neutrophil chemotaxis / RNA splicing / 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 / 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-P8J / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.98 Å
AuthorsKishor, C. / Blanchard, H.
Funding support Australia, 1items
OrganizationGrant numberCountry
Other governmentCancer Council Queensland Grant ID180845 Australia
CitationJournal: Chem.Biol.Drug Des. / Year: 2020
Title: Linear triazole-linked pseudo oligogalactosides as scaffolds for galectin inhibitor development.
Authors: Dussouy, C. / Kishor, C. / Lambert, A. / Lamoureux, C. / Blanchard, H. / Grandjean, C.
History
DepositionAug 2, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 29, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 23, 2020Group: 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
Revision 1.2Mar 13, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)16,2664
Polymers15,7581
Non-polymers5083
Water1,946108
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)35.740, 57.820, 62.590
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: 15758.100 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-P8J / methyl 3-O-[(1-beta-D-galactopyranosyl-1H-1,2,3-triazol-4-yl)methyl]-beta-D-galactopyranoside


Mass: 437.399 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C16H27N3O11 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 108 / 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: 2.02 Å3/Da / Density % sol: 39.24 %
Crystal growTemperature: 297 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: 31% PEG 3100, 100 mM tris-HCl pH 7.5, 100 mM MgCl2, 8 mM 2-Mercaptoethanol

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Australian Synchrotron / Beamline: MX1 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 9, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 1.98→42.48 Å / Num. obs: 9412 / % possible obs: 100 % / Redundancy: 11.5 % / Biso Wilson estimate: 11.613760561 Å2 / Rmerge(I) obs: 0.067 / Net I/σ(I): 27
Reflection shellResolution: 1.99→2.06 Å / Rmerge(I) obs: 0.11 / Num. unique obs: 906

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Processing

Software
NameVersionClassification
PHENIX1.10.1_2155refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.98→42.4712432161 Å / SU ML: 0.183560541566 / Cross valid method: FREE R-VALUE / σ(F): 1.35131633093 / Phase error: 20.7599755456
RfactorNum. reflection% reflection
Rfree0.205321999708 478 5.07862303442 %
Rwork0.164055093778 --
obs0.166373910052 9412 99.9787550457 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso mean: 12.949859417 Å2
Refinement stepCycle: LAST / Resolution: 1.98→42.4712432161 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1112 0 32 108 1252
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.008340151849921243
X-RAY DIFFRACTIONf_angle_d0.9774772277391705
X-RAY DIFFRACTIONf_chiral_restr0.0663176750631191
X-RAY DIFFRACTIONf_plane_restr0.00727594252068227
X-RAY DIFFRACTIONf_dihedral_angle_d11.2340894558775
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.98-2.27340.1923636989351870.1590902392723062X-RAY DIFFRACTION99.9692307692
1.9861-2.27340.2347574762921420.1535739104782919X-RAY DIFFRACTION100
2.2734-2.86420.2122786652461490.1812674452132953X-RAY DIFFRACTION99.9677731228

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