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- PDB-5h9r: Crystal Structure of Human Galectin-3 CRD in Complex with TAZTDG -

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Basic information

Entry
Database: PDB / ID: 5h9r
TitleCrystal Structure of Human Galectin-3 CRD in Complex with TAZTDG
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN / galectin / thio-digalactoside (TDG) / pi-arginine interaction / fluorine bonding
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-TGZ / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.58 Å
AuthorsHsieh, T.J. / Lin, H.Y. / Lin, C.H.
Funding support Taiwan, 3items
OrganizationGrant numberCountry
Academia Sinica Taiwan
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)18,3762
Polymers17,8721
Non-polymers5031
Water2,270126
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area0 Å2
ΔGint0 kcal/mol
Surface area7370 Å2
MethodPISA
Unit cell
Length a, b, c (Å)36.814, 57.690, 62.983
Angle α, β, γ (deg.)90.00, 90.00, 90.00
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 / Plasmid: pET15a
Production host: Escherichia coli 'BL21-Gold(DE3)pLysS AG' (bacteria)
Strain (production host): BL21-Gold(DE3)pLysS AG / References: UniProt: P17931
#2: Chemical ChemComp-TGZ / (2~{S},3~{R},4~{S},5~{R},6~{R})-2-[(2~{S},3~{R},4~{S},5~{R},6~{R})-4-[4-(3-fluorophenyl)-1,2,3-triazol-1-yl]-6-(hydroxymethyl)-3,5-bis(oxidanyl)oxan-2-yl]sulfanyl-6-(hydroxymethyl)oxane-3,4,5-triol


Mass: 503.499 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C20H26FN3O9S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 126 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 1.87 Å3/Da / Density % sol: 34.26 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5 / Details: 0.1 M Tris pH8.5, 0.2 M MgCl2, 30% (w/v) PEG 3350 / PH range: 7.5-8.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13C1 / Wavelength: 0.97622 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 2, 2015
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97622 Å / Relative weight: 1
ReflectionResolution: 1.58→30 Å / Num. obs: 18965 / % possible obs: 99.7 % / Redundancy: 4.6 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 22.8
Reflection shellResolution: 1.58→1.64 Å / Redundancy: 4.4 % / Rmerge(I) obs: 0.447 / Mean I/σ(I) obs: 3.32 / % possible all: 98.2

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
HKL-2000data collection
HKL-2000data processing
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2NMN

2nmn


Resolution: 1.58→26.225 Å / SU ML: 0.14 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 19.03 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.197 1835 10 %Random selection
Rwork0.1695 ---
obs0.1723 18350 96.55 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.58→26.225 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 34 126 1268
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0061181
X-RAY DIFFRACTIONf_angle_d1.2231610
X-RAY DIFFRACTIONf_dihedral_angle_d12.646454
X-RAY DIFFRACTIONf_chiral_restr0.049183
X-RAY DIFFRACTIONf_plane_restr0.006208
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5797-1.62240.2491250.20621129X-RAY DIFFRACTION88
1.6224-1.67010.25611310.1861187X-RAY DIFFRACTION91
1.6701-1.7240.23361310.1881184X-RAY DIFFRACTION93
1.724-1.78560.22231390.17571227X-RAY DIFFRACTION95
1.7856-1.85710.19561400.15791261X-RAY DIFFRACTION96
1.8571-1.94160.16781430.15361262X-RAY DIFFRACTION97
1.9416-2.04390.18191420.15341277X-RAY DIFFRACTION98
2.0439-2.17190.19431420.15621295X-RAY DIFFRACTION99
2.1719-2.33950.18451420.16641291X-RAY DIFFRACTION99
2.3395-2.57470.22461440.16641317X-RAY DIFFRACTION99
2.5747-2.94690.19811490.18171322X-RAY DIFFRACTION99
2.9469-3.71110.19831490.15541352X-RAY DIFFRACTION100
3.7111-26.22910.17991580.18141411X-RAY DIFFRACTION99

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