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Simulation report and files

General information

Name: Spike protein in the Closed state

Included proteins: Spike

Uniprot ID: P0DTC2

Species: Severe acute respiratory syndrome coronavirus 2 (2019-nCoV) (SARS-CoV-2)

PDB ID: 6VXX

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: 72759

Simulation details

Software and version: NAMD 2.14

Forcefield and version: CHARMM36 N/D

Time step : 2.0 fs

Delta : 0.2 ns

Replicates: 1

Accumulated simulation time: 0.5436 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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Spike protein in the Closed state ( 6VXX)

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Non-hydrogen protein atoms
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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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C
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G
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P
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K
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K
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S
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T
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N
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L
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V
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K
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N
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K
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C
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V
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N
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F
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F
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N
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G
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G
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G
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D
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A
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A
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Y
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C
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Y
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T
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S
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S
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I
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I
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Y
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T
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678
M
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S
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L
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G
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A
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E
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N
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679
S
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V(R)
705
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A
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684
Y(R)
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S
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N
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N
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S
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I
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A
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I
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T
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N
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F
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T
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I
720
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S
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V
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T
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T
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E
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I
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L
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P
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V
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S
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M
731
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T
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K
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T
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S
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V
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D
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C
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T
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M
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Y
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D
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S
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T
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S
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N
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L
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L
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L
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Y
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G
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F
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C
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N
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R
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A
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E
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P
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G
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G
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F
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N
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F
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S
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I
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L
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P
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P
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P
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I
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E
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D
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L
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L
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N
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K
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V
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T
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K
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F
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N
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G
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T
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V
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P
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L
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L
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M
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A
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M
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G
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911
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914
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E
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N
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Q
920
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L
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I
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A
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N
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F
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N
928
928
S
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A
930
930
I
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G
932
932
K
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I
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Q
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D
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L
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S
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A
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A
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V
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V
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N
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N
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A
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Q
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A
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L
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N
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960
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V
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S
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N
969
969
F
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970
G
971
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A
972
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I
973
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S
974
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S
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V
976
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L
977
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N
978
978
D
979
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I
980
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L
981
981
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 0/16
Substitution scores
0
 BLOSUM90 score
0
 Δ charge
0
 Epstein's coefficient of difference
0
 Experimental exchangeability
0
 Grantham's distance
0
 Miyata's distance
0
 Sneath's index
0
 Δ hydrophobicity
Conservation
0
 Frequency (‰)
0
 SIFT4G Score
0
 SIFT4G Median IC
Structure
0
 Post-translational modification
0
 Surface accessibility
0
 FoldX ΔΔG
Experimental
0
 Mean Experimental Antibody Escape
0
 Max. Experimental Antibody Escape
Others
Annotation
Time-dependent 0/28
Parameter Average Weight average SD Weight SD
RMSD
0
0

Please select a variant from the sequence above.
RMSF
0
0

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SASA
0
0

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CHI1
0
0

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All contacts
0
0

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Hydrogen bond contacts
0
0

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Salt bridge contacts
0
0

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Hydrophobic contacts
0
0

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Pi-cation contacts
0
0

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Pi-stacking contacts
0
0

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T-stacking contacts
0
0

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Van der Waals contacts
0
0

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Water bridge contacts
0
0

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Extended water bridge contacts
0
0

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User-provided descriptors 0/0

Upload your own descriptors according to this template.