Workbench
Simulation report and files
General information
Name: Fully-glycosylated full-length S protein model (model 6VXX_2_2_1)
Included proteins: Spike
Uniprot ID: P0DTC2
Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)
PDB ID: 6VXX
Submitted by: Lehigh University, Bethlehem (CHARMM-GUI)
Submission date: November 01, 2020
System setup
Ligands: None
Membrane composition:
PSM
DPP
Cholesterol
POP
Solvent type: TIP3P (water was filtered out of the simulation output)
Total number of atoms: 332712
Simulation details
Software and version: GROMACS 2019.2
Forcefield and version: CHARMM36m N/D
Time step : 4.0 fs
Delta : 2.0 ns
Replicates: 1
Accumulated simulation time: 1.2840 µs
References
Woo, H.; Park, S.-J.; Choi, Y.K.; Park, T.; Tanveer, M.; Cao, Y.; Kern, N.R.; Lee, J.; Yeom, M.S.; Croll, T.I.; et al. Developing a Fully Glycosylated Full-Length SARS-CoV-2 Spike Protein Model in a Viral Membrane. J. Phys. Chem. B 2020, 124, 7128–7137. DOI: 10.1021/ACS.JPCB.0C04553
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Fully-glycosylated full-length S protein model (model 6VXX_2_2_1)
( 6VXX)
Selection
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RMSF
Trajectory:
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Stride:
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Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
Variant impact
Select a variant from the sequence to obtain its impact score as well as mutation effect and time-dependent descriptors:
Display isolate:
All isolates
Spike
AA
Seq. pos.
PDB resID
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S
982
982
R
983
983
L
984
984
D
985
985
K
986
986
V
987
987
E
988
988
A
989
989
E
990
990
V
991
991
Q
992
992
I
993
993
D
994
994
R
995
995
L
996
996
I
997
997
T
998
998
G
999
999
R
1000
1000
L
1001
1001
Q
1002
1002
S
1003
1003
L
1004
1004
Q
1005
1005
T
1006
1006
Y
1007
1007
V
1008
1008
T
1009
1009
Q
1010
1010
Q
1011
1011
L
1012
1012
I
1013
1013
R
1014
1014
A
1015
1015
A
1016
1016
E
1017
1017
I
1018
1018
R
1019
1019
A
1020
1020
S
1021
1021
A
1022
1022
N
1023
1023
L
1024
1024
A
1025
1025
A
1026
1026
T
1027
1027
K
1028
1028
M
1029
1029
S
1030
1030
E
1031
1031
C
1032
1032
V
1033
1033
L
1034
1034
G
1035
1035
Q
1036
1036
S
1037
1037
K
1038
1038
R
1039
1039
V
1040
1040
D
1041
1041
F
1042
1042
C
1043
1043
G
1044
1044
K
1045
1045
G
1046
1046
Y
1047
1047
H
1048
1048
L
1049
1049
M
1050
1050
S
1051
1051
F
1052
1052
P
1053
1053
Q
1054
1054
S
1055
1055
A
1056
1056
P
1057
1057
H
1058
1058
G
1059
1059
V
1060
1060
V
1061
1061
F
1062
1062
L
1063
1063
H
1064
1064
V
1065
1065
T
1066
1066
Y
1067
1067
V
1068
1068
P
1069
1069
A
1070
1070
Q
1071
1071
E
1072
1072
K
1073
1073
N
1074
1074
F
1075
1075
T
1076
1076
T
1077
1077
A
1078
1078
P
1079
1079
A
1080
1080
I
1081
1081
C
1082
1082
H
1083
1083
D
1084
1084
G
1085
1085
K
1086
1086
A
1087
1087
H
1088
1088
F
1089
1089
P
1090
1090
R
1091
1091
E
1092
1092
G
1093
1093
V
1094
1094
F
1095
1095
V
1096
1096
S
1097
1097
N
1098
1098
G
1099
1099
T
1100
1100
H
1101
1101
W
1102
1102
F
1103
1103
V
1104
1104
T
1105
1105
Q
1106
1106
R
1107
1107
N
1108
1108
F
1109
1109
Y
1110
1110
E
1111
1111
P
1112
1112
Q
1113
1113
I
1114
1114
I
1115
1115
T
1116
1116
T
1117
1117
D
1118
1118
N
1119
1119
T
1120
1120
F
1121
1121
V
1122
1122
S
1123
1123
G
1124
1124
N
1125
1125
C
1126
1126
D
1127
1127
V
1128
1128
V
1129
1129
I
1130
1130
G
1131
1131
I
1132
1132
V
1133
1133
N
1134
1134
N
1135
1135
T
1136
1136
V
1137
1137
Y
1138
1138
D
1139
1139
P
1140
1140
L
1141
1141
Q
1142
1142
P
1143
1143
E
1144
1144
L
1145
1145
D
1146
1146
S
1147
1147
Impact score
Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.
Mutation effect
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| Substitution scores | ||
|---|---|---|
| BLOSUM90 score | ||
| Δ charge | ||
| Epstein's coefficient of difference | ||
| Experimental exchangeability | ||
| Grantham's distance | ||
| Miyata's distance | ||
| Sneath's index | ||
| Δ hydrophobicity | ||
| Conservation | ||
|---|---|---|
| Frequency (‰) | ||
| SIFT4G Score | ||
| SIFT4G Median IC | ||
| Structure | ||
|---|---|---|
| Post-translational modification | ||
| Surface accessibility | ||
| FoldX ΔΔG | ||
| Experimental | ||
|---|---|---|
| Mean Experimental Antibody Escape | ||
| Max. Experimental Antibody Escape | ||
| Others | ||
|---|---|---|
| Annotation | ||
Time-dependent
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| Parameter | Average | Weight average | SD | Weight SD | |
| RMSD |
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| RMSF |
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| SASA |
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| CHI1 |
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| All contacts |
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| Hydrogen bond contacts |
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| Salt bridge contacts |
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| Hydrophobic contacts |
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| Pi-cation contacts |
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| Pi-stacking contacts |
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| T-stacking contacts |
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| Van der Waals contacts |
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| Water bridge contacts |
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| Extended water bridge contacts |
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Please select a variant from the sequence above. |
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User-provided descriptors
0/0
Upload your own descriptors according to this template.