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Simulation report and files

General information

Name: Apo SARS-CoV-2 PLPro (from PDB 6W9C C-chain)

Included proteins: NSP3

Uniprot ID: P0DTD1

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

PDB ID: 6W9C

Submitted by: Chang group, University of California, Riverside

Submission date: November 03, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: TIP3P (water was filtered out of the simulation output)

Total number of atoms: 4897

Simulation details

Software and version: Amber18 N/D

Forcefield and version: Amber ff14SB N/D

Time step : 2.0 fs

Delta : 0.02 ns

Replicates: 1

Accumulated simulation time: 1.0000 µs

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The interaction network has been generated using Flare Plots, powered by R. Fonseca and A. J. Venkatakrishnan.

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Apo SARS-CoV-2 PLPro (from PDB 6W9C C-chain) ( 6W9C)

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Zinc finger region

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Toolkit

General
Interaction network

Hydrogen bonds

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RMSD
Trajectory:
Frames:
All
From to
Stride:
Reference: frame from trajectory
Selection:
Protein alpha carbons
Protein CA, CB, C, N, O
Non-hydrogen protein atoms
All protein atoms
RMSF
Trajectory:
Frames:
All
From to
Stride:
Selection:
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
NSP3
AA
Seq. pos.
PDB resID
T(I)
749
1
I
750
1
K
751
2
V
752
3
F
753
4
T
754
5
T
755
6
V
756
7
D
757
8
N
758
9
I
759
10
N
760
11
L
761
12
H
762
13
T
763
14
Q
764
15
V
765
16
V
766
17
D
767
18
M
768
19
S
769
20
M
770
21
T
771
22
Y
772
23
G
773
24
Q
774
25
Q
775
26
F
776
27
G
777
28
P
778
29
T
779
30
Y
780
31
L
781
32
D
782
33
G
783
34
A
784
35
D
785
36
V
786
37
T
787
38
K
788
39
I
789
40
K
790
41
P
791
42
H
792
43
N
793
44
S
794
45
H
795
46
E
796
47
G
797
48
K
798
49
T
799
50
F
800
51
Y
801
52
V
802
53
L
803
54
P
804
55
N
805
56
D
806
57
D
807
58
T
808
59
L
809
60
R
810
61
V
811
62
E
812
63
A
813
64
F
814
65
E
815
66
Y
816
67
Y
817
68
H
818
69
T
819
70
T
820
71
D
821
72
P
822
73
S
823
74
F
824
75
L
825
76
G
826
77
R
827
78
Y
828
79
M
829
80
S
830
81
A
831
82
L
832
83
N
833
84
H
834
85
T
835
86
K
836
87
K
837
88
W
838
89
K
839
90
Y
840
91
P
841
92
Q
842
93
V
843
94
N
844
95
G
845
96
L
846
97
T
847
98
S
848
99
I
849
100
K
850
101
W
851
102
A
852
103
D
853
104
N
854
105
N
855
106
C
856
107
Y
857
108
L
858
109
A
859
110
T
860
111
A
861
112
L
862
113
L
863
114
T
864
115
L
865
116
Q
866
117
Q
867
118
I
868
119
E
869
120
L
870
121
K
871
122
F
872
123
N
873
124
P
874
125
P
875
126
A
876
127
L
877
128
Q
878
129
D
879
130
A
880
131
Y
881
132
Y
882
133
R
883
134
A
884
135
R
885
136
A
886
137
G
887
138
E
888
139
A
889
140
A
890
141
N
891
142
F
892
143
C
893
144
A
894
145
L
895
146
I
896
147
L
897
148
A
898
149
Y
899
150
C
900
151
N
901
152
K
902
153
T
903
154
V
904
155
G
905
156
E
906
157
L
907
158
G
908
159
D
909
160
V
910
161
R
911
162
E
912
163
T
913
164
M
914
165
S
915
166
Y
916
167
L
917
168
F
918
169
Q
919
170
H
920
171
A
921
172
N
922
173
L
923
174
D
924
175
S
925
176
C
926
177
K
927
178
R
928
179
V
929
180
L
930
181
N
931
182
V
932
183
V
933
184
C
934
185
K
935
186
T
936
187
C
937
188
G
938
189
Q
939
190
Q
940
191
Q
941
192
T
942
193
T
943
194
L
944
195
K
945
196
G
946
197
V
947
198
E
948
199
A
949
200
V
950
201
M
951
202
Y
952
203
M
953
204
G
954
205
T
955
206
L
956
207
S
957
208
Y
958
209
E
959
210
Q
960
211
F
961
212
K
962
213
K
963
214
G
964
215
V
965
216
Q
966
217
I
967
218
P
968
219
C
971
222
G
972
223
K
973
224
Q
974
225
A
975
226
T
976
227
K
977
228
Y
978
229
L
979
230
V
980
231
Q
981
232
Q
982
233
E
983
234
S
984
235
P
985
236
F
986
237
V
987
238
M
988
239
M
989
240
S
990
241
A
991
242
P
992
243
P
993
244
A
994
245
Q
995
246
Y
996
247
E
997
248
L
998
249
K
999
250
H
1000
251
G
1001
252
T
1002
253
F
1003
254
T
1004
255
C
1005
256
A
1006
257
S
1007
258
E
1008
259
Y
1009
260
T
1010
261
G
1011
262
N
1012
263
Y
1013
264
Q
1014
265
C
1015
266
G
1016
267
H
1017
268
Y
1018
269
K
1019
270
H
1020
271
I
1021
272
T
1022
273
S
1023
274
K
1024
275
E
1025
276
T
1026
277
L
1027
278
Y
1028
279
C
1029
280
I
1030
281
D
1031
282
G
1032
283
A
1033
284
L
1034
285
L
1035
286
T
1036
287
K
1037
288
S
1038
289
S
1039
290
E
1040
291
Y
1041
292
K
1042
293
G
1043
294
P
1044
295
I
1045
296
T
1046
297
D
1047
298
V
1048
299
F
1049
300
Y
1050
301
K
1051
302
E
1052
303
N
1053
304
S
1054
305
Y
1055
306
T
1056
307
T
1057
308
T
1058
309
I
1059
310
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

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

Please select a variant from the sequence above.
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

Please select a variant from the sequence above.
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.