Workbench
General information
Name: Fully-glycosylated S protein (head) in open-closed-closed state in complex with antibody s309
Included proteins: Spike
Uniprot ID: P0DTC2
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6WPT
Submitted by: Lehigh University, Bethlehem (CHARMM-GUI)
Submission date: May 20, 2021
System setup
Ligands: None
Membrane composition: None
Solvent type: TIP3P (water was filtered out of the simulation output)
Total number of atoms: 74769
Simulation details
Software and version: GROMACS 2018.6
Forcefield and version: CHARMM36(m) -
Time step : 4.0 fs
Delta : 1.0 ns
Replicates: 1
Accumulated simulation time: 0.5210 µs
References
Cao, Y.; Choi, Y.K.; Frank, M.; Woo, H.; Park, S.-J.; Yeom, M.S.; Seok, C.; Im, W. Dynamic Interactions of Fully Glycosylated SARS-CoV-2 Spike Protein with Various Antibodies. bioRxiv 2021, 2021.05.10.443519. DOI: 10.1101/2021.05.10.443519
Visualization and trajectory sharing powered by NGL Viewer and MDsrv.
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: