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- PDB-7xfa: Structure of human Galectin-3 CRD in complex with monosaccharide ... -

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Basic information

Entry
Database: PDB / ID: 7xfa
TitleStructure of human Galectin-3 CRD in complex with monosaccharide inhibitor
ComponentsGalectin-3
KeywordsGalactoside-binding lectin / Lectin / galactose / fibrosis / SUGAR BINDING PROTEIN
Function / homology
Function and homology information


: / 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 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 / macrophage chemotaxis / positive regulation of calcium ion import / 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 / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / molecular condensate scaffold activity / 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 / 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-D9J / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 0.98 Å
AuthorsShukla, J. / Raman, S. / Ghosh, K.
Funding support India, 1items
OrganizationGrant numberCountry
Other private India
CitationJournal: J.Med.Chem. / Year: 2022
Title: Identification of Monosaccharide Derivatives as Potent, Selective, and Orally Bioavailable Inhibitors of Human and Mouse Galectin-3.
Authors: Liu, C. / Jalagam, P.R. / Feng, J. / Wang, W. / Raja, T. / Sura, M.R. / Manepalli, R.K.V.L.P. / Aliphedi, B.R. / Medavarapu, S. / Nair, S.K. / Muthalagu, V. / Natesan, R. / Gupta, A. / Beno, ...Authors: Liu, C. / Jalagam, P.R. / Feng, J. / Wang, W. / Raja, T. / Sura, M.R. / Manepalli, R.K.V.L.P. / Aliphedi, B.R. / Medavarapu, S. / Nair, S.K. / Muthalagu, V. / Natesan, R. / Gupta, A. / Beno, B. / Panda, M. / Ghosh, K. / Shukla, J.K. / Sale, H. / Haldar, P. / Kalidindi, N. / Shah, D. / Patel, D. / Mathur, A. / Ellsworth, B.A. / Cheng, D. / Regueiro-Ren, A.
History
DepositionApr 1, 2022Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Oct 12, 2022Provider: repository / Type: Initial release
Revision 1.1Nov 29, 2023Group: 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)19,1872
Polymers18,5651
Non-polymers6211
Water4,306239
1


  • Idetical with deposited unit
  • defined by author
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)36.824, 58.187, 63.118
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: 18565.160 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-D9J / (2~{S},3~{R},4~{R},5~{R},6~{R})-4-[4-[4-chloranyl-3,5-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-2-[2-[5-chloranyl-2-(trifluoromethyl)phenyl]-5-methyl-1,2,4-triazol-3-yl]-6-(hydroxymethyl)oxane-3,5-diol


Mass: 621.343 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C24H19Cl2F5N6O4 / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 239 / 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: 2.06 Å3/Da / Density % sol: 40.41 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop
Details: 28-35% PEG 4000/6000, 0.1M Tris (pH 7.5 - pH 8.5), 0.1M MgCl2, 0.4M NaSCN

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID30B / Wavelength: 0.9763 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Nov 15, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 0.98→36.83 Å / Num. obs: 75866 / % possible obs: 96.5 % / Redundancy: 5.2 % / CC1/2: 0.991 / Rmerge(I) obs: 0.074 / Net I/σ(I): 12.8
Reflection shellResolution: 0.98→1.01 Å / Num. unique obs: 3833 / CC1/2: 0.47

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
PDB_EXTRACT3.27data extraction
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7CXA

7cxa


Resolution: 0.98→14.35 Å / Cor.coef. Fo:Fc: 0.9569 / Cor.coef. Fo:Fc free: 0.9551 / SU R Cruickshank DPI: 0.027 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.029 / SU Rfree Blow DPI: 0.03 / SU Rfree Cruickshank DPI: 0.028
RfactorNum. reflection% reflectionSelection details
Rfree0.2049 3564 4.71 %RANDOM
Rwork0.1911 ---
obs0.1917 75738 96.47 %-
Displacement parametersBiso max: 96.34 Å2 / Biso mean: 12.79 Å2 / Biso min: 4.44 Å2
Baniso -1Baniso -2Baniso -3
1--1.3054 Å20 Å20 Å2
2--0.9307 Å20 Å2
3---0.3747 Å2
Refine analyzeLuzzati coordinate error obs: 0.122 Å
Refinement stepCycle: final / Resolution: 0.98→14.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 60 239 1407
Biso mean--11.5 24.36 -
Num. residues----138
Refine LS restraints
Refine-IDTypeNumberRestraint functionWeightDev ideal
X-RAY DIFFRACTIONt_dihedral_angle_d462SINUSOIDAL2
X-RAY DIFFRACTIONt_trig_c_planes35HARMONIC2
X-RAY DIFFRACTIONt_gen_planes197HARMONIC5
X-RAY DIFFRACTIONt_it1277HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_chiral_improper_torsion164SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact1572SEMIHARMONIC4
X-RAY DIFFRACTIONt_bond_d1277HARMONIC20.01
X-RAY DIFFRACTIONt_angle_deg1774HARMONIC21.17
X-RAY DIFFRACTIONt_omega_torsion5.8
X-RAY DIFFRACTIONt_other_torsion13.31
LS refinement shellResolution: 0.98→1 Å / Rfactor Rfree error: 0 / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3242 182 4.75 %
Rwork0.3174 3650 -
all0.3178 3832 -
obs--96.47 %

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