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Yorodumi- PDB-6qlp: Galectin-3C in complex with substituted polyfluoroaryl monothioga... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qlp | ||||||
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Title | Galectin-3C in complex with substituted polyfluoroaryl monothiogalactoside derivative 3 | ||||||
Components | Galectin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / LECTIN / CARBOHYDRATE-BINDING PROTEIN / GALACTOSE-SPECIFIC LECTIN 3 / GALACTOSIDE-BINDING PROTEIN / GALBP / IGE-6 BINDING PROTEIN / L-31 / LAMININ-BINDING PROTEIN / LECTIN L-29 / MAC-2 | ||||||
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 | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / FOURIER SYNTHESIS / Resolution: 1.081 Å | ||||||
Authors | Kumar, R. / Peterson, K. / Nilsson, U.J. / Logan, D.T. | ||||||
Funding support | Sweden, 1items
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Citation | Journal: Chemmedchem / Year: 2019 Title: Structure and Energetics of Ligand-Fluorine Interactions with Galectin-3 Backbone and Side-Chain Amides: Insight into Solvation Effects and Multipolar Interactions. Authors: Kumar, R. / Ignjatovic, M.M. / Peterson, K. / Olsson, M. / Leffler, H. / Ryde, U. / Nilsson, U.J. / Logan, D.T. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qlp.cif.gz | 108.2 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qlp.ent.gz | 83.3 KB | Display | PDB format |
PDBx/mmJSON format | 6qlp.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qlp_validation.pdf.gz | 688.3 KB | Display | wwPDB validaton report |
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Full document | 6qlp_full_validation.pdf.gz | 689.1 KB | Display | |
Data in XML | 6qlp_validation.xml.gz | 9.7 KB | Display | |
Data in CIF | 6qlp_validation.cif.gz | 13.5 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/6qlp ftp://data.pdbj.org/pub/pdb/validation_reports/ql/6qlp | HTTPS FTP |
-Related structure data
Related structure data | 6qlnC 6qloC 6qlqC 6qlrC 6qlsC 6qltC 6qluC 3zslS S: Starting model for refinement C: citing same article (ref.) |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 15701.049 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: LGALS3, MAC2 / Production host: Escherichia coli BL21(DE3) (bacteria) / References: UniProt: P17931 |
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#2: Chemical | ChemComp-PGE / |
#3: Chemical | ChemComp-J3Q / ( |
#4: Chemical | ChemComp-CL / |
#5: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.07 Å3/Da / Density % sol: 40.5 % |
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Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5 Details: 30% PEG 4000, 0.1 M Tris/HCl pH 7.5, 0.1 M MgCl2, 0.4 M NaSCN, 7.9 mM beta-mercaptoethanol |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9765 Å |
Detector | Type: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: May 7, 2016 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.9765 Å / Relative weight: 1 |
Reflection | Resolution: 1.081→42.26 Å / Num. obs: 55562 / % possible obs: 99.51 % / Redundancy: 4.8 % / CC1/2: 1 / Rmerge(I) obs: 0.05591 / Rpim(I) all: 0.02811 / Rrim(I) all: 0.06284 / Net I/σ(I): 12.17 |
Reflection shell | Resolution: 1.081→1.12 Å / Rmerge(I) obs: 1.851 / CC1/2: 0.212 / Rpim(I) all: 0.9822 / Rrim(I) all: 2.104 |
-Processing
Software |
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Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3zsl Resolution: 1.081→42.26 Å / SU ML: 0.15 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 19.98
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Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.081→42.26 Å
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Refine LS restraints |
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LS refinement shell |
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