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

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Basic information

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


negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / mononuclear cell migration / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis / IgE binding / eosinophil chemotaxis / regulation of extrinsic apoptotic signaling pathway via death domain receptors / signaling receptor inhibitor activity / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / negative regulation of T cell receptor signaling pathway / protein phosphatase inhibitor activity / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / regulation of T cell proliferation / 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 / spliceosomal complex / positive regulation of protein-containing complex assembly / molecular condensate scaffold activity / mRNA processing / carbohydrate binding / protein phosphatase binding / : / mitochondrial inner membrane / innate immune response / Neutrophil degranulation / cell surface / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / nucleus / membrane / 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
piperazine / : / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.12 Å
AuthorsJinal, S. / 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

Downloads & links

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Assembly

Deposited unit
A: Galectin-3
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)40,7797
Polymers39,3312
Non-polymers1,4495
Water4,576254
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: light scattering
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area7350 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-8 kcal/mol
Surface area7410 Å2
MethodPISA
Unit cell
Length a, b, c (Å)34.350, 43.340, 48.150
Angle α, β, γ (deg.)111.12, 105.87, 90.42
Int Tables number1
Space group name H-MP1

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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


Mass: 19665.328 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / 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-SXP / 2-[(2S,3R,4S,5R,6R)-2-[2-[2,5-bis(chloranyl)phenyl]-5-methyl-1,2,4-triazol-3-yl]-4-[4-[4-chloranyl-3,5-bis(fluoranyl)phenyl]-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-5-oxidanyl-oxan-3-yl]oxyethanoic acid


Mass: 645.827 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C25H21Cl3F2N6O6 / Feature type: SUBJECT OF INVESTIGATION
#4: Chemical ChemComp-PZE / piperazine


Mass: 86.136 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10N2 / Feature type: SUBJECT OF INVESTIGATION
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 254 / 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: 1.62 Å3/Da / Density % sol: 24.26 %
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: 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: 1.12→50 Å / Num. obs: 77739 / % possible obs: 85.7 % / Redundancy: 1.7 % / Rsym value: 0.037 / Net I/σ(I): 9.4
Reflection shellResolution: 1.12→1.15 Å / Num. unique obs: 81792 / Rsym value: 0.26

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Processing

Software
NameVersionClassification
REFMAC5.8.0189refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.12→37.11 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.961 / SU B: 0.618 / SU ML: 0.03 / Cross valid method: THROUGHOUT / ESU R: 0.045 / ESU R Free: 0.046 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.21097 4052 5 %RANDOM
Rwork0.19316 ---
obs0.19406 77739 85.87 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 15.515 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å2-0.04 Å20.03 Å2
2---0 Å20.1 Å2
3---0 Å2
Refinement stepCycle: 1 / Resolution: 1.12→37.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2213 0 90 254 2557
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0260.022391
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg2.311.9993263
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6785284
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.44323.982113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.16315392
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3711518
X-RAY DIFFRACTIONr_chiral_restr0.1570.2357
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.0212046
X-RAY DIFFRACTIONr_gen_planes_other
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_it1.5651.2971112
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.0621.9551390
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.8121.5681279
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined7.92419.8613413
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.12→1.149 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.275 293 -
Rwork0.257 5393 -
obs--80.01 %

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