data_6VXX {ClusTorus}

6VXX: Structure of the SARS-CoV-2 spike glycoprotein(closed state)

Description

The torsion angle dataset of SARS-CoV-2 spike glycopreotein.

Usage

data_6VXX

Format

data_6VXX consists of following informations:

phi

main chain torsion angle for atoms C,N,CA,C.

psi

main chain torsion angle for atoms N,CA,C,N.

omega

main chain torsion angle for atoms CA,C,N,CA.

alpha

virtual torsion angle between consecutive C-alpha atoms.

chi1

side chain torsion angle for atoms N,CA,CB,*G.

chi2

side chain torsion angle for atoms CA,CB,*G,*D.

chi3

side chain torsion angle for atoms CB,*G,*D,*E.

chi4

side chain torsion angle for atoms *G,*D,*E,*Z.

chi5

side chain torsion angle for atoms *D,*E,*Z, NH1.

coords

numeric matrix of ‘justified’ coordinates.

tbl

a numeric matrix of psi, phi and chi torsion angles.

Source

This data can be downloaded in https://www.rcsb.org/structure/6VXX, or with using R package bio3d. Precisely, we use the code: bio3d::torsion.pdb(bio3d::read.pdb("6vxx"))

References

Walls, A. C., Park, Y. J., Tortorici, M. A., Wall, A., McGuire, A. T., & Veesler, D. (2020). Structure, function, and antigenicity of the SARS-CoV-2 spike glycoprotein. Cell, 181(2), 281-292. Retrived from https://www.wwpdb.org/pdb?id=pdb_00006vxx

See Also

Description of the angluar information is from the 'value' part of torsion.pdb in the package bio3d.