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- PDB-8iu1: Crystal structure of mouse Galectin-3 in complex with small molec... -

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Basic information

Entry
Database: PDB / ID: 8iu1
TitleCrystal structure of mouse Galectin-3 in complex with small molecule inhibitor
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / Fibrosis / Galactose
Function / homology
Function and homology information


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 / cornified envelope / negative regulation of endocytosis / IgE binding / negative regulation of T cell receptor signaling pathway / immunological synapse / glial cell projection / Neutrophil degranulation / extracellular matrix organization ...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 / cornified envelope / negative regulation of endocytosis / IgE binding / negative regulation of T cell receptor signaling pathway / immunological synapse / glial cell projection / Neutrophil degranulation / extracellular matrix organization / extracellular matrix / RNA splicing / skeletal system development / spliceosomal complex / mRNA processing / : / carbohydrate binding / cell differentiation / innate immune response / external side of plasma membrane / cell surface / extracellular space / extracellular region / nucleus / 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: 1.97 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)17,0603
Polymers16,4551
Non-polymers6052
Water1,76598
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area60 Å2
ΔGint-4 kcal/mol
Surface area7320 Å2
Unit cell
Length a, b, c (Å)110.670, 110.670, 110.670
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number199
Space group name H-MI213
Components on special symmetry positions
IDModelComponents
11A-302-

MG

21A-474-

HOH

31A-498-

HOH

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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 / IgE-binding protein / L-34 galactoside-binding lectin / Laminin-binding protein / Lectin L-29 / Mac-2 antigen


Mass: 16454.906 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: Lgals3 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: P16110
#2: 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
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 98 / 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: 3.43 Å3/Da / Density % sol: 64.16 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop
Details: 32% PEG 4000, 0.1M TRIS(8.0), 0.4M NASCN, 0.1M MGCL2

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1.0332 Å
DetectorType: RAYONIX MX300-HS / Detector: CCD / Date: Jun 30, 2017
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0332 Å / Relative weight: 1
ReflectionResolution: 1.97→35 Å / Num. obs: 16076 / % possible obs: 99.9 % / Redundancy: 20.1 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 24.6
Reflection shellResolution: 1.97→2.02 Å / Rmerge(I) obs: 0.038

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Processing

Software
NameVersionClassification
XDSdata reduction
Aimlessdata scaling
REFMAC5.8.0049refinement
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.97→35 Å / Cor.coef. Fo:Fc: 0.974 / Cor.coef. Fo:Fc free: 0.961 / SU B: 3.409 / SU ML: 0.092 / Cross valid method: THROUGHOUT / ESU R: 0.12 / ESU R Free: 0.123 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.215 754 4.7 %RANDOM
Rwork0.173 ---
obs0.175 15322 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.74 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.97→35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1103 0 38 98 1239
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.021168
X-RAY DIFFRACTIONr_bond_other_d00.0118
X-RAY DIFFRACTIONr_angle_refined_deg2.3761.981586
X-RAY DIFFRACTIONr_angle_other_deg0.829340
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.8335137
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.97123.79358
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.12915191
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.3081510
X-RAY DIFFRACTIONr_chiral_restr0.1820.2172
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.0211003
X-RAY DIFFRACTIONr_gen_planes_other0.0010.027
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_it5.1475.102552
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it5.7167.579687
X-RAY DIFFRACTIONr_mcangle_other5.7137.578688
X-RAY DIFFRACTIONr_scbond_it7.0275.565614
X-RAY DIFFRACTIONr_scbond_other7.0215.564615
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other9.648.146900
X-RAY DIFFRACTIONr_long_range_B_refined10.30743.3381661
X-RAY DIFFRACTIONr_long_range_B_other10.26543.1241638
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.97→2.02 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.345 56 -
Rwork0.316 1119 -
obs--100 %

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