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- PDB-8itz: Crystal structure of human Galectin-3 in complex with small molec... -

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Basic information

Entry
Database: PDB / ID: 8itz
TitleCrystal structure of human Galectin-3 in complex with small molecule inhibitor
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Fibrosis / Galactose
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
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.22 Å
AuthorsJinal, S. / Amit, K. / Ghosh, K.
Funding support1items
OrganizationGrant numberCountry
Other private
CitationJournal: To Be Published
Title: Discovery and Exploration of Monosaccharide Linked Dimers to Target Fibrosis
Authors: Swidorski, J.J. / Beno, B.B. / Liu, C. / Yoon, D. / Ghosh, K. / Sale, H. / Shah, D. / Acharya, K. / Yanchunas, J. / Ellsworth, B. / Cheng, D. / Regueiro-Ren, A.
History
DepositionMar 23, 2023Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Mar 27, 2024Provider: repository / Type: Initial release

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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)19,9874
Polymers19,3481
Non-polymers6393
Water3,621201
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area150 Å2
ΔGint-11 kcal/mol
Surface area7320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.510, 57.241, 61.257
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: 19347.986 Da / Num. of mol.: 1 / Mutation: P106H, Y107M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: P17931
#2: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-QB2 / 2-[(2R,3R,4S,5R,6R)-2-(3,4-dichlorophenyl)sulfanyl-6-(hydroxymethyl)-5-oxidanyl-4-[4-[3,4,5-tris(fluoranyl)phenyl]-1,2,3-triazol-1-yl]oxan-3-yl]oxyethanoic acid


Mass: 580.361 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C22H18Cl2F3N3O6S / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 201 / 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: 1.65 Å3/Da / Density % sol: 25.64 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: BUFFER = 0.1M TRIS (7.8), SALT= NASCN; PRECIPITANT = PEG 6K

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-D / Wavelength: 1.1271 Å
DetectorType: DECTRIS EIGER X 9M / Detector: PIXEL / Date: Apr 5, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.1271 Å / Relative weight: 1
ReflectionResolution: 1.2→61.26 Å / Num. obs: 35805 / % possible obs: 91 % / Redundancy: 6.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 16.6
Reflection shellResolution: 1.22→1.25 Å / Rmerge(I) obs: 0.06

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0049refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.22→41.82 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.948 / SU B: 1.154 / SU ML: 0.023 / Cross valid method: THROUGHOUT / ESU R: 0.046 / ESU R Free: 0.044 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.173 1782 5 %RANDOM
Rwork0.147 ---
obs0.148 33966 90.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 13.52 Å2
Baniso -1Baniso -2Baniso -3
1--0.37 Å20 Å20 Å2
2---0.08 Å20 Å2
3---0.46 Å2
Refinement stepCycle: LAST / Resolution: 1.22→41.82 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1095 0 39 201 1335
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.021167
X-RAY DIFFRACTIONr_bond_other_d0.0010.021116
X-RAY DIFFRACTIONr_angle_refined_deg1.9721.9941592
X-RAY DIFFRACTIONr_angle_other_deg0.93732554
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4535139
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.56324.07454
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.19615187
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.229158
X-RAY DIFFRACTIONr_chiral_restr0.1450.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211416
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02276
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.2611.037554
X-RAY DIFFRACTIONr_mcbond_other1.2471.033552
X-RAY DIFFRACTIONr_mcangle_it1.5291.561690
X-RAY DIFFRACTIONr_mcangle_other1.5281.561691
X-RAY DIFFRACTIONr_scbond_it2.3951.341613
X-RAY DIFFRACTIONr_scbond_other2.3941.341614
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other2.6591.916902
X-RAY DIFFRACTIONr_long_range_B_refined3.27811.0411355
X-RAY DIFFRACTIONr_long_range_B_other2.6869.7761230
X-RAY DIFFRACTIONr_rigid_bond_restr4.80232283
X-RAY DIFFRACTIONr_sphericity_free19.292542
X-RAY DIFFRACTIONr_sphericity_bonded8.28952415
LS refinement shellResolution: 1.22→1.25 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.338 51 -
Rwork0.385 1132 -
obs--41.61 %

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