[English] 日本語
Yorodumi- PDB-6qlu: Galectin-3C in complex with fluoroaryltriazole monothiogalactosid... -
+Open data
-Basic information
Entry | Database: PDB / ID: 6qlu | ||||||
---|---|---|---|---|---|---|---|
Title | Galectin-3C in complex with fluoroaryltriazole monothiogalactoside derivative-8 | ||||||
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 protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / eosinophil chemotaxis ...negative regulation of protein tyrosine phosphatase activity / negative regulation of immunological synapse formation / RUNX2 regulates genes involved in differentiation of myeloid cells / negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell / regulation of T cell apoptotic process / mononuclear cell migration / IgE binding / positive regulation of mononuclear cell migration / negative regulation of endocytosis / 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 / macrophage chemotaxis / regulation of T cell proliferation / 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 / molecular condensate scaffold activity / neutrophil chemotaxis / RNA splicing / secretory granule membrane / positive regulation of protein-containing complex assembly / negative regulation of extrinsic apoptotic signaling pathway / positive regulation of protein localization to plasma membrane / spliceosomal complex / mRNA processing / carbohydrate binding / collagen-containing extracellular matrix / protein phosphatase binding / 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 / FOURIER SYNTHESIS / Resolution: 1.1 Å | ||||||
Authors | Kumar, R. / Peterson, K. / Nilsson, U.J. / Logan, D.T. | ||||||
Funding support | Sweden, 1items
| ||||||
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 |
|
-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
---|
-Downloads & links
-Download
PDBx/mmCIF format | 6qlu.cif.gz | 108.9 KB | Display | PDBx/mmCIF format |
---|---|---|---|---|
PDB format | pdb6qlu.ent.gz | 83.5 KB | Display | PDB format |
PDBx/mmJSON format | 6qlu.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/ql/6qlu ftp://data.pdbj.org/pub/pdb/validation_reports/ql/6qlu | HTTPS FTP |
---|
-Related structure data
Related structure data | 6qlnC 6qloC 6qlpC 6qlqC 6qlrC 6qlsC 6qltC 3zslS S: Starting model for refinement C: citing same article (ref.) |
---|---|
Similar structure data |
-Links
-Assembly
Deposited unit |
| ||||||||
---|---|---|---|---|---|---|---|---|---|
1 |
| ||||||||
Unit cell |
|
-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 |
---|---|
#2: Chemical | ChemComp-J62 / ( |
#3: Chemical | ChemComp-CL / |
#4: Water | ChemComp-HOH / |
-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
---|
-Sample preparation
Crystal | Density Matthews: 2.16 Å3/Da / Density % sol: 43 % |
---|---|
Crystal grow | Temperature: 298 K / Method: vapor diffusion, hanging drop 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 |
---|---|
Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-3 / Wavelength: 0.95 Å |
Detector | Type: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 21, 2015 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 0.95 Å / Relative weight: 1 |
Reflection | Resolution: 1.1→27.611 Å / Num. obs: 55014 / % possible obs: 99.53 % / Redundancy: 5.7 % / Biso Wilson estimate: 7.3 Å2 / CC1/2: 1 / Rmerge(I) obs: 0.04813 / Rpim(I) all: 0.02198 / Rrim(I) all: 0.05305 / Net I/σ(I): 22.33 |
Reflection shell | Resolution: 1.1→1.139 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.4378 / Mean I/σ(I) obs: 2.84 / CC1/2: 0.852 / Rpim(I) all: 0.2447 / Rrim(I) all: 0.5044 / % possible all: 96.01 |
-Processing
Software |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Refinement | Method to determine structure: FOURIER SYNTHESIS Starting model: 3zsl Resolution: 1.1→27.611 Å / SU ML: 0.08 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 12.46
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Solvent computation | Shrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 1.1→27.611 Å
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Refine LS restraints |
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
LS refinement shell |
|