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- PDB-3t1m: Crystal structure of human galectin-3 carbohydrate recognition do... -

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Basic information

Entry
Database: PDB / ID: 3t1m
TitleCrystal structure of human galectin-3 carbohydrate recognition domain in complex with methyl 3-deoxy-2-O-toluoyl-3-N-toluoyl-beta-D-talopyranoside
ComponentsGalectin-3
KeywordsSUGAR BINDING PROTEIN/INHIBITOR / beta sandwich / SUGAR BINDING PROTEIN-INHIBITOR complex
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 / positive chemotaxis / regulation of T cell proliferation / 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 / spliceosomal complex / molecular condensate scaffold activity / 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. / Jelly Rolls - #200 / Concanavalin A-like lectin/glucanase domain superfamily / Jelly Rolls / Sandwich / Mainly Beta
Similarity search - Domain/homology
Chem-DQT / Galectin-3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.55 Å
AuthorsBlanchard, H. / Collins, P.M.
CitationJournal: Chem.Biol.Drug Des. / Year: 2012
Title: Taloside inhibitors of galectin-1 and galectin-3
Authors: Collins, P.M. / Oberg, C.T. / Leffler, H. / Nilsson, U.J. / Blanchard, H.
History
DepositionJul 22, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Dec 28, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 3, 2013Group: Database references
Revision 1.2Nov 8, 2017Group: Refinement description / Category: software
Revision 1.3Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)16,5193
Polymers16,0541
Non-polymers4652
Water3,009167
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)37.062, 58.369, 63.805
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: 16054.424 Da / Num. of mol.: 1
Fragment: carbohydrate-recognition domain, UNP residues 108-250
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-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-DQT / methyl 3-deoxy-2-O-(4-methylbenzoyl)-3-[(4-methylbenzoyl)amino]-beta-D-talopyranoside / methyl 3-deoxy-2-O-4-toluoyl-3-(4-toluoyl)amino-beta-D-talopyranoside


Mass: 429.463 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C23H27NO7
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 167 / 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: 2.15 Å3/Da / Density % sol: 42.77 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 31% PEG 6000, 100mM MGCl2, 8mM beta merceptoethanol, 100mM Tris-HCL, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 293 K
Diffraction sourceSource: ROTATING ANODE / Type: MACSCIENCE / Wavelength: 1.5418 Å
DetectorType: BRUKER SMART 6000 / Detector: CCD / Date: Aug 12, 2009
RadiationMonochromator: Osmic Mirrors / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.55→43.07 Å / Num. all: 20208 / Num. obs: 19087 / % possible obs: 97.13 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2
Reflection shellResolution: 1.55→1.59 Å / % possible all: 83.3

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Processing

Software
NameVersionClassification
PROTEUM PLUSPLUSdata collection
REFMAC5.5.0109refinement
SAINTdata reduction
SCALAdata scaling
RefinementMethod to determine structure: FOURIER SYNTHESIS / Resolution: 1.55→43.07 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.942 / SU B: 2.704 / SU ML: 0.045 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R Free: 0.081 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1926 1034 5.1 %RANDOM
Rwork0.1599 ---
all0.18 20208 --
obs0.16154 19087 97.13 %-
Solvent computationSolvent model: BABINET MODEL PARAMETERS FOR MASK CACLULATION
Displacement parametersBiso mean: 17.18 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å20 Å2
2---0.54 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 1.55→43.07 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1101 0 32 167 1300
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.0221211
X-RAY DIFFRACTIONr_bond_other_d0.0010.02836
X-RAY DIFFRACTIONr_angle_refined_deg1.2711.9771652
X-RAY DIFFRACTIONr_angle_other_deg0.74932034
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.565147
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.27223.7162
X-RAY DIFFRACTIONr_dihedral_angle_3_deg10.63515204
X-RAY DIFFRACTIONr_dihedral_angle_4_deg11.3531511
X-RAY DIFFRACTIONr_chiral_restr0.0810.2181
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0211355
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02256
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_it2.2884710
X-RAY DIFFRACTIONr_mcbond_other0.7424280
X-RAY DIFFRACTIONr_mcangle_it3.55461165
X-RAY DIFFRACTIONr_scbond_it2.9683501
X-RAY DIFFRACTIONr_scangle_it4.6734.5483
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.55→1.59 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.28 62 -
Rwork0.238 1001 -
obs--71.78 %
Refinement TLS params.Method: refined / Origin x: 13.278 Å / Origin y: 0.8365 Å / Origin z: 6.5209 Å
111213212223313233
T0.0097 Å20.0014 Å2-0.0041 Å2-0.0088 Å20.0052 Å2--0.0092 Å2
L0.5474 °20.1629 °2-0.1831 °2-0.8873 °2-0.3309 °2--0.8514 °2
S0.0234 Å °0.0006 Å °-0.0303 Å °-0.0004 Å °-0.0149 Å °0.0289 Å °0.0571 Å °0.0398 Å °-0.0086 Å °

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