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Yorodumi- PDB-7p5g: NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506... -
+Open data
-Basic information
Entry | Database: PDB / ID: 7p5g | |||||||||
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Title | NMR structure of a peptide deriving from SARS-CoV-2 S RBD 482-506 fragment in HFIP/H2O | |||||||||
Components | Spike glycoprotein | |||||||||
Keywords | ANTIVIRAL PROTEIN / SARS-CoV-2 / mimicking peptides / Spike / Receptor Binding Domain / Covid-19 | |||||||||
Function / homology | Function and homology information Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell ...Maturation of spike protein / viral translation / Translation of Structural Proteins / Virion Assembly and Release / host cell surface / host extracellular space / suppression by virus of host tetherin activity / Induction of Cell-Cell Fusion / structural constituent of virion / entry receptor-mediated virion attachment to host cell / host cell endoplasmic reticulum-Golgi intermediate compartment membrane / membrane fusion / receptor-mediated endocytosis of virus by host cell / Attachment and Entry / positive regulation of viral entry into host cell / receptor-mediated virion attachment to host cell / receptor ligand activity / symbiont-mediated suppression of host innate immune response / host cell surface receptor binding / fusion of virus membrane with host plasma membrane / fusion of virus membrane with host endosome membrane / viral envelope / virion attachment to host cell / SARS-CoV-2 activates/modulates innate and adaptive immune responses / host cell plasma membrane / virion membrane / identical protein binding / membrane / plasma membrane Similarity search - Function | |||||||||
Biological species | Severe acute respiratory syndrome coronavirus 2 | |||||||||
Method | SOLUTION NMR / torsion angle dynamics | |||||||||
Authors | Santoro, A. / Buonocore, M. / Grimaldi, M. / D'Ursi, A.M. | |||||||||
Funding support | 1items
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Citation | Journal: Heliyon / Year: 2022 Title: Structural analysis of a simplified model reproducing SARS-CoV-2 S RBD/ACE2 binding site. Authors: Buonocore, M. / Santoro, A. / Grimaldi, M. / Covelli, V. / Firoznezhad, M. / Rodriquez, M. / Santin, M. / D'Ursi, A.M. | |||||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 7p5g.cif.gz | 241.6 KB | Display | PDBx/mmCIF format |
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PDB format | pdb7p5g.ent.gz | 171.1 KB | Display | PDB format |
PDBx/mmJSON format | 7p5g.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 7p5g_validation.pdf.gz | 437.1 KB | Display | wwPDB validaton report |
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Full document | 7p5g_full_validation.pdf.gz | 604.9 KB | Display | |
Data in XML | 7p5g_validation.xml.gz | 17.5 KB | Display | |
Data in CIF | 7p5g_validation.cif.gz | 29.2 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/p5/7p5g ftp://data.pdbj.org/pub/pdb/validation_reports/p5/7p5g | HTTPS FTP |
-Related structure data
Related structure data | 7p55C 7p5qC 7p5sC C: citing same article (ref.) |
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Similar structure data | Similarity search - Function & homologyF&H Search |
Other databases |
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-Links
-Assembly
Deposited unit |
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1 |
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NMR ensembles |
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-Components
#1: Protein/peptide | Mass: 2772.996 Da / Num. of mol.: 1 / Source method: obtained synthetically Source: (synth.) Severe acute respiratory syndrome coronavirus 2 References: UniProt: P0DTC2 |
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-Experimental details
-Experiment
Experiment | Method: SOLUTION NMR | ||||||||||||||||||||||||
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NMR experiment |
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-Sample preparation
Details | Type: solution Contents: 2.5 mM SMIMIC-OR, 50 % v/v Hexafluoroisopropanol, 40 % v/v H2O, 10 % v/v [U-100% 2H] D2O, 50% hexafluoroisopropanol/40% H2O/10% D2O Label: SMIMIC / Solvent system: 50% hexafluoroisopropanol/40% H2O/10% D2O | ||||||||||||||||||||
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Sample |
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Sample conditions | Ionic strength: 0 Not defined / Label: conditions_1 / pH: 2.5 / PH err: 0.1 / Pressure: 1 atm / Temperature: 298 K |
-NMR measurement
NMR spectrometer | Type: Bruker AVANCE II / Manufacturer: Bruker / Model: AVANCE II / Field strength: 500 MHz |
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-Processing
NMR software |
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Refinement | Method: torsion angle dynamics / Software ordinal: 3 | |||||||||||||||
NMR representative | Selection criteria: lowest energy | |||||||||||||||
NMR ensemble | Conformer selection criteria: target function / Conformers calculated total number: 100 / Conformers submitted total number: 38 |