General information
Name: NSP12-NSP7-NSP8 - SARS-CoV-2 Polymerase
Included proteins: NSP8, NSP12, NSP7
Uniprot ID: P0DTD1
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6M71
Submitted by: Exscalate4CoV
Submission date: September 23, 2020
System setup
Ligands: None
Membrane composition: None
Solvent type: TIP3P
Total number of atoms: 138650
Simulation details
Software and version: GROMACS 2020
Forcefield and version: AMBER 99
Time step : 1.0 fs
Delta : 0.1 ns
Replicates: 1
Accumulated simulation time: 2.6462 µs
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The interaction network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.
Metal ion-binding site
Region of interest
Repeat
Domain of interest
Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:
Selected:
Selected:
Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.
Substitution scores | ||
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BLOSUM90 score | |
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Δ charge | |
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Epstein's coefficient of difference | |
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Experimental exchangeability | |
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Grantham's distance | |
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Miyata's distance | |
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Sneath's index | |
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Δ hydrophobicity |
Conservation | ||
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Frequency (‰) | |
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SIFT4G Score | |
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SIFT4G Median IC |
Structure | ||
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Post-translational modification | |
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Surface accessibility | |
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FoldX ΔΔG |
Experimental | ||
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Mean Experimental Antibody Escape | |
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Max. Experimental Antibody Escape |
Others | ||
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Annotation |
Parameter | Average | Weight average | SD | Weight SD | |
RMSD |
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RMSF |
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Please select a variant from the sequence above. RMSF of residue (ResID , chain ) |
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SASA |
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Please select a variant from the sequence above. SASA of residue (ResID , chain ) |
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CHI1 |
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Please select a variant from the sequence above. CHI1 of residue (ResID , chain ) |
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All contacts |
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Please select a variant from the sequence above. All contacts of residue (ResID , chain ) |
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Hydrogen bond contacts |
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Please select a variant from the sequence above. Hydrogen bond contacts of residue (ResID , chain ) |
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Salt bridge contacts |
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Please select a variant from the sequence above. Salt bridge contacts of residue (ResID , chain ) |
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Hydrophobic contacts |
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Please select a variant from the sequence above. Hydrophobic contacts of residue (ResID , chain ) |
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Pi-cation contacts |
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Please select a variant from the sequence above. Pi-cation contacts of residue (ResID , chain ) |
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Pi-stacking contacts |
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Please select a variant from the sequence above. Pi-stacking contacts of residue (ResID , chain ) |
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T-stacking contacts |
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Please select a variant from the sequence above. T-stacking contacts of residue (ResID , chain ) |
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Van der Waals contacts |
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Please select a variant from the sequence above. Van der Waals contacts of residue (ResID , chain ) |
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Water bridge contacts |
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Please select a variant from the sequence above. Water bridge contacts of residue (ResID , chain ) |
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Extended water bridge contacts |
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Please select a variant from the sequence above. Extended water bridge contacts of residue (ResID , chain ) |
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Score