Workbench
General information
Name: Spike protein in the Open state (N165A / N234A mutations)
Included proteins: Spike
Uniprot ID: P0DTC2
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6VSB
Submitted by: Amaro Lab
Submission date: October 28, 2020
System setup
Ligands: None
Membrane composition: None
Solvent type: TIP3P (water was filtered out of the simulation output)
Total number of atoms: 71294
Simulation details
Software and version: NAMD 2.14
Forcefield and version: CHARMM36 N/D
Time step : 2.0 fs
Delta : 0.3 ns
Replicates: 1
Accumulated simulation time: 1.0014 µs
References
Casalino, L.; Gaieb, Z.; Goldsmith, J.A.; Hjorth, C.K.; Dommer, A.C.; Harbison, A.M.; Fogarty, C.A.; Barros, E.P.; Taylor, B.C.; McLellan, J.S.; et al. Beyond Shielding: The Roles of Glycans in SARS-CoV-2 Spike Protein. bioRxiv 2020, 2020.06.11.146522. DOI: 10.1101/2020.06.11.146522
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The interaction network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.
Viewer
Selection
Site of interest
Region of interest
Coiled-coil region
Domain of interest
Toolkit
Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors: