+Open data
-Basic information
Entry | Database: PDB / ID: 4bm8 | ||||||
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Title | Galectin-3c in complex with Bisamido-thiogalactoside derivate 3 | ||||||
Components | GALECTIN-3 | ||||||
Keywords | SUGAR BINDING PROTEIN / IGE-BINDING PROTEIN / LECTIN | ||||||
Function / homology | Function and homology information negative regulation of protein tyrosine phosphatase activity / 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 / negative regulation of endocytosis / IgE binding / positive regulation of mononuclear cell migration ...negative regulation of protein tyrosine phosphatase activity / 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 / negative regulation of endocytosis / IgE binding / 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 / regulation of T cell proliferation / positive chemotaxis / positive regulation of calcium ion import / chemoattractant activity / macrophage chemotaxis / monocyte chemotaxis / Advanced glycosylation endproduct receptor signaling / ficolin-1-rich granule membrane / immunological synapse / laminin binding / epithelial cell differentiation / RNA splicing / neutrophil chemotaxis / 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 / 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: 0.96 Å | ||||||
Authors | Noresson, A.L. / Oberg, C.T. / Engstrom, O. / Hakansson, M. / Logan, D.T. / Leffler, H. / Nilsson, U.J. | ||||||
Citation | Journal: 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 |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 4bm8.cif.gz | 94.7 KB | Display | PDBx/mmCIF format |
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PDB format | pdb4bm8.ent.gz | 70.8 KB | Display | PDB format |
PDBx/mmJSON format | 4bm8.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 4bm8_validation.pdf.gz | 736.8 KB | Display | wwPDB validaton report |
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Full document | 4bm8_full_validation.pdf.gz | 739.7 KB | Display | |
Data in XML | 4bm8_validation.xml.gz | 12.6 KB | Display | |
Data in CIF | 4bm8_validation.cif.gz | 19 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/bm/4bm8 ftp://data.pdbj.org/pub/pdb/validation_reports/bm/4bm8 | HTTPS FTP |
-Related structure data
Related structure data | 4bliC 4bljC 3zslS C: citing same article (ref.) S: Starting model for refinement |
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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: 15675.012 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 |
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#2: Chemical | ChemComp-A6J / ( |
#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: 1.73 Å3/Da / Density % sol: 29.5 % |
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Crystal grow | pH: 7.5 Details: 19 MG/ML GALECTIN-3C, 100MM NACL, 29 % W/V PEG 4000, 0.4 M NASCN, 18 MM BETA-MERCAPTOETHANOL,0.02 % NAN3, 10 MM PHOSHATE, 100 MM MGCL2, 100 MM TRIS/HCL PH 7.5, 2.5 MM LIGAND |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: MAX II / Beamline: I911-2 / Wavelength: 1.04077 |
Detector | Type: MARRESEARCH / Detector: CCD / Date: Sep 7, 2011 / Details: MULTILAYER MIRRORS |
Radiation | Monochromator: BENT SILICON CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.04077 Å / Relative weight: 1 |
Reflection | Resolution: 0.96→30 Å / Num. obs: 79320 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 5.2 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 20.9 |
Reflection shell | Resolution: 0.96→0.98 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.56 / Mean I/σ(I) obs: 2 / % possible all: 92.3 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: PDB ENTRY 3ZSL Resolution: 0.96→20 Å / Num. parameters: 15022 / Num. restraintsaints: 20174 / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH AND HUBER
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Refine analyze | Num. disordered residues: 77 / Occupancy sum hydrogen: 1143 / Occupancy sum non hydrogen: 1463.5 | |||||||||||||||||||||||||||||||||
Refinement step | Cycle: LAST / Resolution: 0.96→20 Å
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Refine LS restraints |
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