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Yorodumi- PDB-6qgf: Galectin-3C in complex with a pair of enantiomeric ligands: R ena... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qgf | ||||||
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Title | Galectin-3C in complex with a pair of enantiomeric ligands: R enantiomer | ||||||
Components | Galectin-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / cell signalling drug design conformational entropy | ||||||
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 / epithelial cell differentiation / laminin binding / neutrophil chemotaxis / positive regulation of protein localization to plasma membrane / RNA splicing / secretory granule membrane / molecular condensate scaffold activity / negative regulation of extrinsic apoptotic signaling pathway / spliceosomal complex / positive regulation of protein-containing complex assembly / mRNA processing / protein phosphatase binding / carbohydrate 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 / cytoplasm / cytosol Similarity search - Function | ||||||
Biological species | Homo sapiens (human) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.34 Å | ||||||
Authors | Manzoni, F. / Verteramo, M.L. / Oksanen, E. / Nilsson, U.J. / Logan, D.T. | ||||||
Funding support | Sweden, 1items
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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 | 6qgf.cif.gz | 119.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb6qgf.ent.gz | 84.1 KB | Display | PDB format |
PDBx/mmJSON format | 6qgf.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 6qgf_validation.pdf.gz | 638.5 KB | Display | wwPDB validaton report |
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Full document | 6qgf_full_validation.pdf.gz | 638.9 KB | Display | |
Data in XML | 6qgf_validation.xml.gz | 10.4 KB | Display | |
Data in CIF | 6qgf_validation.cif.gz | 15.1 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/qg/6qgf ftp://data.pdbj.org/pub/pdb/validation_reports/qg/6qgf | HTTPS FTP |
-Related structure data
Related structure data | 6qgeC 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-J0T / ( |
#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: 2.08 Å3/Da / Density % sol: 40.92 % |
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Crystal grow | Temperature: 295 K / Method: vapor diffusion / pH: 7.5 Details: 28% (w/v) PEG 4000, Tris-HCl pH 7.5, 0.4 M NaSCN, 15 mM beta-mercaptoethanol. Drop volume was 2 microlitres and the protein solution:reservoir ratio was varied between 0.5:1, 1:1, and 2:1. ...Details: 28% (w/v) PEG 4000, Tris-HCl pH 7.5, 0.4 M NaSCN, 15 mM beta-mercaptoethanol. 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 ligand for 7 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: 1.34→42.52 Å / Num. obs: 29677 / % possible obs: 98.1 % / Redundancy: 5.7 % / Biso Wilson estimate: 8.37 Å2 / CC1/2: 0.997 / Rmerge(I) obs: 0.117 / Rpim(I) all: 0.052 / Rrim(I) all: 0.128 / Net I/σ(I): 13.5 / Num. measured all: 170528 | ||||||||||||||||||||||||
Reflection shell | Diffraction-ID: 1
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-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 3ZSJ Resolution: 1.34→42.5 Å / SU ML: 0.128 / Cross valid method: THROUGHOUT / σ(F): 1.36 / Phase error: 14.5632
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Solvent computation | Shrinkage radii: 0.4 Å / VDW probe radii: 0.8 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters | Biso mean: 12.11 Å2 | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.34→42.5 Å
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Refine LS restraints |
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LS refinement shell |
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