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- PDB-7cxa: Structure of human Galectin-3 CRD in complex with TD-139 belongin... -

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Basic information

Entry
Database: PDB / ID: 7cxa
TitleStructure of human Galectin-3 CRD in complex with TD-139 belonging to P31 space group.
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / beta-galactose binding protein / CARBOHYDRATE / TD-139
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 / negative regulation of endocytosis / IgE binding / 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 / negative regulation of endocytosis / IgE binding / 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 / 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. / Concanavalin A-like lectin/glucanase domain superfamily
Similarity search - Domain/homology
Chem-TD2 / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.97 Å
AuthorsKumar, A.
CitationJournal: Glycobiology / Year: 2021
Title: Molecular mechanism of interspecies differences in the binding affinity of TD139 to Galectin-3.
Authors: Kumar, A. / Paul, M. / Panda, M. / Jayaram, S. / Kalidindi, N. / Sale, H. / Vetrichelvan, M. / Gupta, A. / Mathur, A. / Beno, B. / Regueiro-Ren, A. / Cheng, D. / Ramarao, M. / Ghosh, K.
History
DepositionSep 1, 2020Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 1, 2021Provider: repository / Type: Initial release
Revision 1.1Feb 16, 2022Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Nov 29, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id ..._struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id

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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)38,4986
Polymers37,1302
Non-polymers1,3684
Water1,874104
1
A: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2493
Polymers18,5651
Non-polymers6842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area130 Å2
ΔGint-10 kcal/mol
Surface area7280 Å2
MethodPISA
2
B: Galectin-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,2493
Polymers18,5651
Non-polymers6842
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area140 Å2
ΔGint-11 kcal/mol
Surface area7330 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.843, 40.843, 152.631
Angle α, β, γ (deg.)90.000, 90.000, 120.000
Int Tables number144
Space group name H-MP31
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: _ / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: MET / End label comp-ID: MET / Refine code: _ / Auth seq-ID: 114 - 249 / Label seq-ID: 29 - 164

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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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.: 2 / Fragment: Carbohydrare Recognition Domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Plasmid: pET28 N-His-TVMV / Details (production host): pET28 N-His-TVMV / Production host: Escherichia coli (E. coli) / 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-TD2 / 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-beta-D-galactopyranosyl 3-deoxy-3-[4-(3-fluorophenyl)-1H-1,2,3-triazol-1-yl]-1-thio-beta-D-galactopyranoside


Mass: 648.635 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C28H30F2N6O8S / Feature type: SUBJECT OF INVESTIGATION
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 104 / 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: 1.98 Å3/Da / Density % sol: 37.86 %
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: CLSI / Beamline: 08ID-1 / Wavelength: 0.9795 Å
DetectorType: RAYONIX MX-300 / Detector: CCD / Date: Sep 5, 2014
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
Reflection twin
Crystal-IDIDOperatorDomain-IDFraction
11H, K, L10.035
11K, H, -L20.322
11-h,-k,l30.606
11-K, -H, -L40.038
ReflectionResolution: 1.97→50 Å / Num. obs: 20163 / % possible obs: 99.7 % / Redundancy: 4.3 % / Rmerge(I) obs: 0.063 / Χ2: 1.046 / Net I/σ(I): 12.2 / Num. measured all: 86610
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique obsΧ2Diffraction-ID% possible all
1.97-2.044.40.73820571.0251100
2.04-2.124.40.52519651.125199.9
2.12-2.224.50.39320201.0471100
2.22-2.344.40.26620221.048199.9
2.34-2.484.50.19919931.051100
2.48-2.674.50.14320581.0111100
2.67-2.944.30.11220501.011100
2.94-3.3740.0820141.0231100
3.37-4.2440.05719981.0491100
4.24-5040.04719861.079196.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0258refinement
HKL-2000data scaling
PDB_EXTRACT3.25data extraction
HKL-2000data reduction
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ZSL

3zsl


Resolution: 1.97→32.09 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.952 / SU B: 6.398 / SU ML: 0.19 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.042 / ESU R Free: 0.035 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT U VALUES : REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2351 1119 5.6 %RANDOM
Rwork0.2022 ---
obs0.2042 19011 99.62 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 136.58 Å2 / Biso mean: 62.585 Å2 / Biso min: 29.81 Å2
Baniso -1Baniso -2Baniso -3
1-20.71 Å20 Å20 Å2
2--20.71 Å20 Å2
3----41.42 Å2
Refinement stepCycle: final / Resolution: 1.97→32.09 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2134 0 152 104 2390
Biso mean--65.57 63.33 -
Num. residues----275
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0122285
X-RAY DIFFRACTIONr_bond_other_d00.0160
X-RAY DIFFRACTIONr_angle_refined_deg1.4311.6993124
X-RAY DIFFRACTIONr_angle_other_deg0.633132
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3285273
X-RAY DIFFRACTIONr_dihedral_angle_2_deg40.9222.137117
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.26215335
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.8461515
X-RAY DIFFRACTIONr_chiral_restr0.1080.2307
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.022026
X-RAY DIFFRACTIONr_gen_planes_other0.0010.0220
Refine LS restraints NCS

Ens-ID: 1 / Number: 3879 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.08 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 1.97→2.019 Å / Rfactor Rfree error: 0
RfactorNum. reflection% reflection
Rfree0.383 86 -
Rwork0.28 1428 -
obs--100 %

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