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Yorodumi- PDB-2lvz: Solution structure of a Eosinophil Cationic Protein-trisaccharide... -
+Open data
-Basic information
Entry | Database: PDB / ID: 2lvz | |||||||||
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Title | Solution structure of a Eosinophil Cationic Protein-trisaccharide heparin mimetic complex | |||||||||
Components | Eosinophil cationic protein | |||||||||
Keywords | HYDROLASE / heparin / molecular recognition | |||||||||
Function / homology | Function and homology information induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide ...induction of bacterial agglutination / Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters / RNA catabolic process / Antimicrobial peptides / RNA nuclease activity / innate immune response in mucosa / lipopolysaccharide binding / chemotaxis / azurophil granule lumen / antimicrobial humoral immune response mediated by antimicrobial peptide / antibacterial humoral response / endonuclease activity / defense response to Gram-negative bacterium / nucleic acid binding / defense response to Gram-positive bacterium / innate immune response / Neutrophil degranulation / extracellular space / extracellular region Similarity search - Function | |||||||||
Biological species | Homo sapiens (human) | |||||||||
Method | SOLUTION NMR / molecular dynamics | |||||||||
Model details | lowest energy, model1 | |||||||||
Authors | Garcia Mayoral, M. / Canales, A. / Diaz, D. / Lopez Prados, J. / Moussaoui, M. / de Paz, J. / Angulo, J. / Nieto, P. / Jimenez Barbero, J. / Boix, E. / Bruix, M. | |||||||||
Citation | Journal: Acs Chem.Biol. / Year: 2013 Title: Insights into the glycosaminoglycan-mediated cytotoxic mechanism of eosinophil cationic protein revealed by NMR. Authors: Garcia-Mayoral, M.F. / Canales, A. / Diaz, D. / Lopez-Prados, J. / Moussaoui, M. / de Paz, J.L. / Angulo, J. / Nieto, P.M. / Jimenez-Barbero, J. / Boix, E. / Bruix, M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 2lvz.cif.gz | 877.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb2lvz.ent.gz | 743 KB | Display | PDB format |
PDBx/mmJSON format | 2lvz.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 2lvz_validation.pdf.gz | 526.3 KB | Display | wwPDB validaton report |
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Full document | 2lvz_full_validation.pdf.gz | 703 KB | Display | |
Data in XML | 2lvz_validation.xml.gz | 85.9 KB | Display | |
Data in CIF | 2lvz_validation.cif.gz | 97.7 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/lv/2lvz ftp://data.pdbj.org/pub/pdb/validation_reports/lv/2lvz | HTTPS FTP |
-Related structure data
Similar structure data | |
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Other databases |
-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein | Mass: 15598.876 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Homo sapiens (human) / Gene: RNASE3, ECP, RNS3 / Production host: Escherichia coli (E. coli) References: UniProt: P12724, Hydrolases; Acting on ester bonds; Endoribonucleases producing 3'-phosphomonoesters |
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#2: Polysaccharide | 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid- ...2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranose-(1-4)-2-O-sulfo-alpha-L-idopyranuronic acid-(1-4)-propan-2-yl 2-deoxy-6-O-sulfo-2-(sulfoamino)-alpha-D-glucopyranoside Type: oligosaccharide / Mass: 958.848 Da / Num. of mol.: 1 Source method: isolated from a genetically manipulated source |
-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Contents: 0.5 mM [U-13C; U-15N] Eosinophil Cationic Protein, 0.5 mM Heparin (3-MER), 100 mM potassium phosphate, 300 mM potassium chloride, 90% H2O/10% D2O Solvent system: 90% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0.3 / pH: 4 / Pressure: ambient / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker Avance / Manufacturer: Bruker / Model: AVANCE / Field strength: 800 MHz |
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-Processing
NMR software |
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Refinement | Method: molecular dynamics / Software ordinal: 1 | ||||||||||||||||||
NMR representative | Selection criteria: lowest energy | ||||||||||||||||||
NMR ensemble | Conformer selection criteria: structures with the lowest energy Conformers calculated total number: 100 / Conformers submitted total number: 20 |