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- PDB-5h9p: Crystal Structure of Human Galectin-3 CRD in Complex with TD139 -

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Basic information

Entry
Database: PDB / ID: 5h9p
TitleCrystal Structure of Human Galectin-3 CRD in Complex with TD139
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / galectin / thio-digalactoside (TDG) / pi-arginine interaction
Function / homology
Function and homology information


negative regulation of NK T cell activation / 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 / receptor ligand inhibitor activity / positive regulation of mononuclear cell migration / negative regulation of endocytosis ...negative regulation of NK T cell activation / 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 / 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 / RUNX1 regulates transcription of genes involved in differentiation of myeloid cells / signaling receptor inhibitor activity / 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 / immunological synapse / ficolin-1-rich granule membrane / laminin binding / neutrophil chemotaxis / epithelial cell differentiation / 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 / cytoplasm / cytosol
Similarity search - Function
Galectin-like / Galactoside-binding lectin / Galectin / Galectin, carbohydrate recognition domain / Galactoside-binding lectin / Galactoside-binding lectin (galectin) domain profile. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-TD2 / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.04 Å
AuthorsHsieh, T.J. / Lin, H.Y. / Lin, C.H.
Funding support Taiwan, 2items
OrganizationGrant numberCountry
Ministry of Science and Technology102-2113-M-001-001-MY3 Taiwan
Ministry of Science and Technology102-2923-M-001-001-MY3 Taiwan
CitationJournal: Sci Rep / Year: 2016
Title: Dual thio-digalactoside-binding modes of human galectins as the structural basis for the design of potent and selective inhibitors
Authors: Hsieh, T.J. / Lin, H.Y. / Tu, Z. / Lin, T.C. / Wu, S.C. / Tseng, Y.Y. / Liu, F.T. / Danny Hsu, S.T. / Lin, C.H.
History
DepositionDec 29, 2015Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 29, 2016Provider: repository / Type: Initial release
Revision 1.1Jul 27, 2016Group: Database references
Revision 1.2Nov 8, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_oper_list
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_oper_list.symmetry_operation

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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)18,5212
Polymers17,8721
Non-polymers6491
Water1,51384
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7470 Å2
MethodPISA
Unit cell
Length a, b, c (Å)37.168, 57.145, 63.651
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: 17872.418 Da / Num. of mol.: 1
Fragment: carbohydrate-recognition domain, UNP residues 113-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P17931
#2: 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.: 1 / Source method: obtained synthetically / Formula: C28H30F2N6O8S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 84 / Source method: isolated from a natural source / Formula: H2O

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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: 1.89 Å3/Da / Density % sol: 34.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8 / Details: 0.1 M Tris pH 8.0, 0.2 M LiSO4, 30% (w/v) PEG 4000 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Nov 17, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.04→30 Å / Num. obs: 9047 / % possible obs: 99 % / Redundancy: 10.5 % / Rmerge(I) obs: 0.071 / Rpim(I) all: 0.022 / Rrim(I) all: 0.074 / Χ2: 1.021 / Net I/av σ(I): 30.541 / Net I/σ(I): 15.2 / Num. measured all: 95013
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allCC1/2Rpim(I) allRrim(I) allΧ2% possible all
2.04-2.117.80.3558320.9640.1240.3780.99495.1
2.11-2.28.80.298840.9740.0960.3061.00797.4
2.2-2.39.90.2778740.980.0880.2911.03499.1
2.3-2.42110.2158820.9910.0650.2251.02199.8
2.42-2.5711.50.1829040.9940.0540.191.016100
2.57-2.7711.70.139100.9970.0380.1351.03799.9
2.77-3.0511.60.0849100.9980.0250.0881.04100
3.05-3.4911.50.0569110.9990.0170.0591.034100
3.49-4.39110.0489380.9990.0150.051.00599.7
4.39-3010.10.039100210.0120.0411.00999.4

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Processing

Software
NameVersionClassification
HKL-2000data collection
HKL-2000data scaling
PHENIX1.9_1692refinement
PDB_EXTRACT3.15data extraction
PHENIXdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMN

2nmn


Resolution: 2.04→26.067 Å / SU ML: 0.2 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 21.4 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.195 887 10.05 %
Rwork0.1653 7937 -
obs0.1684 8824 96.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso max: 78.19 Å2 / Biso mean: 27.7415 Å2 / Biso min: 11.81 Å2
Refinement stepCycle: final / Resolution: 2.04→26.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 45 84 1237
Biso mean--41.16 35.28 -
Num. residues----138
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0051184
X-RAY DIFFRACTIONf_angle_d1.0251612
X-RAY DIFFRACTIONf_chiral_restr0.039171
X-RAY DIFFRACTIONf_plane_restr0.005207
X-RAY DIFFRACTIONf_dihedral_angle_d28.846493
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 6

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.0367-2.16430.24341340.18591163129788
2.1643-2.33130.241440.17221284142895
2.3313-2.56570.20361460.17411323146998
2.5657-2.93650.23081480.17011344149299
2.9365-3.6980.19651530.154413761529100
3.698-26.06880.16361620.163114471609100

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