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Yorodumi- PDB-6qge: Galectin-3C in complex with a pair of enantiomeric ligands: S ena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qge | |||||||||
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Title | Galectin-3C in complex with a pair of enantiomeric ligands: S enantiomer | |||||||||
Components | Galectin-3 | |||||||||
Keywords | SUGAR BINDING PROTEIN / cell signalling drug design conformational entropy | |||||||||
Function / homology | Function and homology information negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / 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 / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / 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 / disaccharide binding / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / negative regulation of endocytosis / positive regulation of mononuclear cell migration / 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 / positive regulation of calcium ion import / macrophage chemotaxis / 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 / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / 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 / extracellular space / RNA binding / extracellular exosome / extracellular region / nucleoplasm / membrane / nucleus / plasma membrane / cytosol / cytoplasm Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.16 Å | |||||||||
Authors | Manzoni, F. / Verteramo, M.L. / Oksanen, E. / Nilsson, U.J. / Logan, D.T. | |||||||||
Funding support | Sweden, 2items
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Citation | Journal: J. Am. Chem. Soc. / Year: 2019 Title: Interplay between Conformational Entropy and Solvation Entropy in Protein-Ligand Binding. Authors: Verteramo, M.L. / Stenstrom, O. / Ignjatovic, M.M. / Caldararu, O. / Olsson, M.A. / Manzoni, F. / Leffler, H. / Oksanen, E. / Logan, D.T. / Nilsson, U.J. / Ryde, U. / Akke, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 6qge.cif.gz | 136.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qge.ent.gz | 89.8 KB | Display | PDB format |
PDBx/mmJSON format | 6qge.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/6qge ftp://data.pdbj.org/pub/pdb/validation_reports/qg/6qge | HTTPS FTP |
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-Related structure data
Related structure data | 6qgfC 3zsjS 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 (E. coli) / References: UniProt: P17931 |
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#2: Chemical | ChemComp-J1E / ( |
#3: 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: 2.1 Å3/Da / Density % sol: 41.33 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: Hanging drop vapour diffusion: 28% (w/v) PEG 4000, Tris-HCl pH 7.5, 0.4 M NaSCN, 15 mM beta-mercaptoethanol. The drop volume was 2 microlitres and the protein solution:reservoir ratio was ...Details: Hanging drop vapour diffusion: 28% (w/v) PEG 4000, Tris-HCl pH 7.5, 0.4 M NaSCN, 15 mM beta-mercaptoethanol. The drop volume was 2 microlitres and the protein solution:reservoir ratio was varied between 0.5:1, 1:1, and 2:1. The crystals were soaked in 10 mM of the ligand for 20 hours. |
-Data collection
Diffraction | Mean temperature: 100 K / Serial crystal experiment: N |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 1 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 27, 2014 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 1.16→31.46 Å / Num. obs: 46420 / % possible obs: 99.9 % / Redundancy: 5.5 % / Biso Wilson estimate: 9.18 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rpim(I) all: 0.027 / Rrim(I) all: 0.065 / Net I/σ(I): 19.1 |
Reflection shell | Resolution: 1.16→1.2 Å / Redundancy: 3.3 % / Rmerge(I) obs: 0.756 / Mean I/σ(I) obs: 1.7 / Num. unique obs: 4567 / CC1/2: 0.618 / Rpim(I) all: 0.487 / Rrim(I) all: 0.903 / % possible all: 99.6 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZSJ Resolution: 1.16→31.46 Å / SU ML: 0.0875 / Cross valid method: THROUGHOUT / σ(F): 1.33 / Phase error: 14.4139
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Solvent computation | Shrinkage radii: 0.7 Å / VDW probe radii: 1 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 14.83 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.16→31.46 Å
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Refine LS restraints |
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LS refinement shell |
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