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- PDB-6tf6: Human galectin-3c in complex with a galactose derivative -

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Basic information

Entry
Database: PDB / ID: 6tf6
TitleHuman galectin-3c in complex with a galactose derivative
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN
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 / 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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-N62 / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsNilsson, U.J. / Zetterberg, F. / Hakansson, M. / Logan, D.T.
Funding support Sweden, 1items
OrganizationGrant numberCountry
Swedish Research Council621-2012-2978 Sweden
CitationJournal: Molecules / Year: 2019
Title: 3-Substituted 1-Naphthamidomethyl-C-galactosyls Interact with Two Unique Sub-sites for High-Affinity and High-Selectivity Inhibition of Galectin-3.
Authors: Dahlqvist, A. / Mandal, S. / Peterson, K. / Hakansson, M. / Logan, D.T. / Zetterberg, F.R. / Leffler, H. / Nilsson, U.J.
History
DepositionNov 13, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Nov 18, 2020Provider: repository / Type: Initial release
Revision 1.1Dec 1, 2021Group: Database references / Category: citation / citation_author / database_2
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Jan 24, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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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)16,3664
Polymers15,7351
Non-polymers6303
Water2,828157
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area240 Å2
ΔGint-17 kcal/mol
Surface area7160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)35.850, 57.340, 62.040
Angle α, β, γ (deg.)90.000, 90.000, 90.000
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: 15735.129 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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-N62 / ~{N}-[[(2~{S},3~{S},4~{R},5~{S},6~{R})-4-[[5,6-bis(fluoranyl)-2-oxidanylidene-chromen-3-yl]methoxy]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]methyl]-4-fluoranyl-naphthalene-1-carboxamide


Mass: 559.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H24F3NO8 / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 157 / 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: 2.03 Å3/Da / Density % sol: 39.3 %
Crystal growTemperature: 300 K / Method: vapor diffusion, hanging drop
Details: 20 MG/ML GALECTIN-3C, 100MM NACL, 30 % W/V PEG 4000, 0.4 M NASCN, 10 MM BETA-MERCAPTOETHANOL, 10 MM PHOSHATE, 100 MM MGCL2, 100 MM TRIS/HCL PH 7.5, 4.5 MM LIGAND

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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: Dec 19, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→31.02 Å / Num. obs: 20755 / % possible obs: 98.8 % / Redundancy: 3.6 % / Rsym value: 0.073 / Net I/σ(I): 12.6
Reflection shellResolution: 1.5→1.54 Å / Num. unique obs: 1522 / Rsym value: 0.725

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Processing

Software
NameVersionClassification
XDSdata reduction
XSCALEdata scaling
REFMAC5.7.0032refinement
PDB_EXTRACT3.25data extraction
REFMAC5phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSM

3zsm


Resolution: 1.5→31.02 Å / Cor.coef. Fo:Fc: 0.98 / Cor.coef. Fo:Fc free: 0.961 / SU B: 2.89 / SU ML: 0.047 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.081 / ESU R Free: 0.072
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.1743 1038 5 %RANDOM
Rwork0.1165 ---
obs0.1194 19717 98.76 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso max: 86.38 Å2 / Biso mean: 15.578 Å2 / Biso min: 6.64 Å2
Baniso -1Baniso -2Baniso -3
1-0.06 Å20 Å20 Å2
2---0.25 Å20 Å2
3---0.19 Å2
Refinement stepCycle: final / Resolution: 1.5→31.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1106 0 42 157 1305
Biso mean--21.96 33.43 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.0191297
X-RAY DIFFRACTIONr_bond_other_d0.0010.021260
X-RAY DIFFRACTIONr_angle_refined_deg2.081.9921774
X-RAY DIFFRACTIONr_angle_other_deg1.52832912
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.5485156
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.94424.77667
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.62615235
X-RAY DIFFRACTIONr_dihedral_angle_4_deg9.069159
X-RAY DIFFRACTIONr_chiral_restr0.1440.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.0211474
X-RAY DIFFRACTIONr_gen_planes_other0.0040.02313
X-RAY DIFFRACTIONr_rigid_bond_restr4.58432557
X-RAY DIFFRACTIONr_sphericity_free44.662563
X-RAY DIFFRACTIONr_sphericity_bonded10.27152614
LS refinement shellResolution: 1.502→1.541 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 72 -
Rwork0.173 1374 -
all-1446 -
obs--96.27 %

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