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- PDB-3t1l: Crystal structure of human Galectin-3 in complex with methyl 2-O-... -

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Basic information

Entry
Database: PDB / ID: 3t1l
TitleCrystal structure of human Galectin-3 in complex with methyl 2-O-acetyl-3-O-toluoyl-beta-D-talopyranoside
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN/INHIBITOR / beta sandwich / SUGAR BINDING PROTEIN-INHIBITOR complex
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 / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding ...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 / 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 / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-MQT / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.6 Å
AuthorsBlanchard, H. / Collins, P.M.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Taloside inhibitors of galectin-1 and galectin-3
Authors: Collins, P.M. / Oberg, C.T. / Leffler, H. / Nilsson, U.J. / Blanchard, H.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Jul 29, 2020Group: Data collection / Derived calculations / Category: chem_comp / struct_site / struct_site_gen / Item: _chem_comp.mon_nstd_flag / _chem_comp.type / Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.4Mar 20, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2
Item: _chem_comp.pdbx_synonyms / _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)16,4443
Polymers16,0541
Non-polymers3902
Water2,216123
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.788, 58.125, 63.541
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: 16054.424 Da / Num. of mol.: 1
Fragment: Carbohdyrate recognition domain, UNP residues 108-250
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.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Sugar ChemComp-MQT / methyl 2-O-acetyl-3-O-(4-methylbenzoyl)-beta-D-talopyranoside / methyl 6-deoxy-1-seleno-beta-L-galactopyranoside / methyl 2-O-acetyl-3-O-(4-methylbenzoyl)-beta-D-taloside / methyl 2-O-acetyl-3-O-(4-methylbenzoyl)-D-taloside / methyl 2-O-acetyl-3-O-(4-methylbenzoyl)-taloside


Type: D-saccharide / Mass: 354.352 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C17H22O8
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 123 / 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: 2.12 Å3/Da / Density % sol: 41.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 31% PEG 6000, 100mM MGCl2, 8mM beta merceptoethanol, 100mM Tris HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 8, 2009
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.6→42.89 Å / Num. obs: 17607 / % possible obs: 94.23 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.6→1.642 Å / % possible all: 75

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
REFMAC5.5.0109refinement
SAINTdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.6→42.89 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.941 / SU B: 2.875 / SU ML: 0.046 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.088 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.18878 893 5.1 %RANDOM
Rwork0.1532 ---
all0.16 ---
obs0.155 16625 94.23 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 19.516 Å2
Baniso -1Baniso -2Baniso -3
1-0.54 Å20 Å20 Å2
2---0.37 Å20 Å2
3----0.17 Å2
Refinement stepCycle: LAST / Resolution: 1.6→42.89 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 26 123 1257
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221234
X-RAY DIFFRACTIONr_bond_other_d0.0010.02865
X-RAY DIFFRACTIONr_angle_refined_deg1.2731.9741690
X-RAY DIFFRACTIONr_angle_other_deg0.73632116
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3915158
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.01123.7162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.57815216
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.2571511
X-RAY DIFFRACTIONr_chiral_restr0.0770.2188
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211376
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02254
X-RAY DIFFRACTIONr_mcbond_it2.424725
X-RAY DIFFRACTIONr_mcbond_other0.7574287
X-RAY DIFFRACTIONr_mcangle_it3.81461197
X-RAY DIFFRACTIONr_scbond_it2.9793509
X-RAY DIFFRACTIONr_scangle_it4.5854.5482
LS refinement shellResolution: 1.6→1.642 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.205 31 -
Rwork0.196 929 -
obs--72.18 %
Refinement TLS params.Method: refined / Origin x: 12.9803 Å / Origin y: 0.6908 Å / Origin z: 6.5517 Å
111213212223313233
T0.0082 Å20.0027 Å2-0.0063 Å2-0.0128 Å20.0105 Å2--0.022 Å2
L0.5667 °20.2393 °2-0.2379 °2-0.9632 °2-0.6291 °2--1.4099 °2
S0.0363 Å °0.0049 Å °-0.0462 Å °0.0058 Å °-0.0082 Å °0.0269 Å °0.0643 Å °0.0525 Å °-0.0281 Å °

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