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- PDB-4bli: Galectin-3c in complex with Bisamido-thiogalactoside derivate 1 -

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Basic information

Entry
Database: PDB / ID: 4bli
TitleGalectin-3c in complex with Bisamido-thiogalactoside derivate 1
ComponentsGALECTIN-3
KeywordsIMMUNE SYSTEM / LECTIN / SUGAR BINDING PROTEIN
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 / regulation of T cell proliferation / positive chemotaxis / 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 / molecular condensate scaffold activity / 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 / 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-GMK / Galectin-3
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.08 Å
AuthorsNoresson, A.L. / Oberg, C.T. / Engstrom, O. / Hakansson, M. / Logan, D.T. / Leffler, H. / Nilsson, U.J.
CitationJournal: To be Published
Title: Controlling Protein Conformation Through Electronic Fine-Tuning of Arginine-Arene Interactions: Synthetic, Structural, and Biological Studies
Authors: Noresson, A.L. / Oberg, C.T. / Engstrom, O. / Hakansson, M. / Logan, D.T. / Leffler, H. / Nilsson, U.J.
History
DepositionMay 3, 2013Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 21, 2014Provider: repository / Type: Initial release
Revision 1.1Jan 17, 2018Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _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)16,4402
Polymers15,7351
Non-polymers7051
Water5,170287
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)36.020, 58.050, 62.380
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: 15735.129 Da / Num. of mol.: 1 / Fragment: CARBOHYDRATE RECOGNITION DOMAIN, RESIDUES 114-250
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: P17931
#2: Chemical ChemComp-GMK / (3-Deoxy-3-(3-methoxy-benzamido)-b-D-galactopyranosyl)-(3-deoxy-3-(3-methoxy-benzamido)-2-O-sulfo-b-D-galactopyranosyl)-sulfide


Mass: 704.720 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C28H36N2O15S2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 287 / 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: 2.1 Å3/Da / Density % sol: 41 %
Description: RIGID BODY REFINEMENT COULD BE STARTED DIRECTLY FROM MODEL 1A3K WIHOUT DOING MR USING A SPECIFIC PROGRAM.
Crystal growpH: 7.5
Details: 19 MG/ML GALECTIN-3C, 100MM NACL, 0.1 M TRIS/HCL PH 7.5, 29 % PEG 4000, 0.4 M NASCN, 18 MM BETA-MERCAPTOETHANOL, 5 MM COMPOUND GMK

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.0379
DetectorType: MARRESEARCH MAR 165 / Detector: CCD / Date: Sep 25, 2008 / Details: MIRRORS
RadiationMonochromator: BENT SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0379 Å / Relative weight: 1
ReflectionResolution: 1.08→30 Å / Num. obs: 56420 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.04 / Net I/σ(I): 22.2
Reflection shellResolution: 1.08→1.11 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.12 / Mean I/σ(I) obs: 10.2 / % possible all: 97.5

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Processing

Software
NameClassification
SHELXL-97refinement
XDSdata reduction
SHELXLdata scaling
XSCALEdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1A3K

1a3k


Resolution: 1.08→30 Å / Num. parameters: 14932 / Num. restraintsaints: 20690 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
RfactorNum. reflection% reflectionSelection details
Rfree0.1416 2820 5.3 %RANDOM
all0.1083 53600 --
obs0.1064 -99.2 %-
Refine analyzeNum. disordered residues: 54 / Occupancy sum hydrogen: 1158 / Occupancy sum non hydrogen: 1432
Refinement stepCycle: LAST / Resolution: 1.08→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1109 0 47 287 1443
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONs_bond_d0.014
X-RAY DIFFRACTIONs_angle_d0.032
X-RAY DIFFRACTIONs_similar_dist0
X-RAY DIFFRACTIONs_from_restr_planes0.0351
X-RAY DIFFRACTIONs_zero_chiral_vol0.096
X-RAY DIFFRACTIONs_non_zero_chiral_vol0.081
X-RAY DIFFRACTIONs_anti_bump_dis_restr0.04
X-RAY DIFFRACTIONs_rigid_bond_adp_cmpnt0.005
X-RAY DIFFRACTIONs_similar_adp_cmpnt0.048
X-RAY DIFFRACTIONs_approx_iso_adps0.111

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