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Workbench

Simulation report and files

General information

Name: PL-PRO

Included proteins: NSP3

Uniprot ID: P0DTD1

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

PDB ID: 6W9C

Submitted by: Exscalate4CoV

Submission date: August 31, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 4894

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: 1.6706 µs

Simulation protocol & starting files

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.

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PL-PRO ( 6W9C)

Selection

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Zinc finger region

Domain of interest

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Input your selection using the NGL selection language.

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
749
4
I
750
5
K
751
6
V
752
7
F
753
8
T
754
9
T
755
10
V
756
11
D
757
12
N
758
13
I
759
14
N
760
15
L
761
16
H
762
17
T
763
18
Q
764
19
V
765
20
V
766
21
D
767
22
M
768
23
S
769
24
M
770
25
T
771
26
Y
772
27
G
773
28
Q
774
29
Q
775
30
F
776
31
G
777
32
P
778
33
T
779
34
Y
780
35
L
781
36
D
782
37
G
783
38
A
784
39
D
785
40
V
786
41
T
787
42
K
788
43
I
789
44
K
790
45
P
791
46
H
792
47
N
793
48
S
794
49
H
795
50
E
796
51
G
797
52
K
798
53
T
799
54
F
800
55
Y
801
56
V
802
57
L
803
58
P
804
59
N
805
60
D
806
61
D
807
62
T
808
63
L
809
64
R
810
65
V
811
66
E
812
67
A
813
68
F
814
69
E
815
70
Y
816
71
Y
817
72
H
818
73
T
819
74
T
820
75
D
821
76
P
822
77
S
823
78
F
824
79
L
825
80
G
826
81
R
827
82
Y
828
83
M
829
84
S
830
85
A
831
86
L
832
87
N
833
88
H
834
89
T
835
90
K
836
91
K
837
92
W
838
93
K
839
94
Y
840
95
P
841
96
Q
842
97
V
843
98
N
844
99
G
845
100
L
846
101
T
847
102
S
848
103
I
849
104
K
850
105
W
851
106
A
852
107
D
853
108
N
854
109
N
855
110
C
856
111
Y
857
112
L
858
113
A
859
114
T
860
115
A
861
116
L
862
117
L
863
118
T
864
119
L
865
120
Q
866
121
Q
867
122
I
868
123
E
869
124
L
870
125
K
871
126
F
872
127
N
873
128
P
874
129
P
875
130
A
876
131
L
877
132
Q
878
133
D
879
134
A
880
135
Y
881
136
Y
882
137
R
883
138
A
884
139
R
885
140
A
886
141
G
887
142
E
888
143
A
889
144
A
890
145
N
891
146
F
892
147
C
893
148
A
894
149
L
895
150
I
896
151
L
897
152
A
898
153
Y
899
154
C
900
155
N
901
156
K
902
157
T
903
158
V
904
159
G
905
160
E
906
161
L
907
162
G
908
163
D
909
164
V
910
165
R
911
166
E
912
167
T
913
168
M
914
169
S
915
170
Y
916
171
L
917
172
F
918
173
Q
919
174
H
920
175
A
921
176
N
922
177
L
923
178
D
924
179
S
925
180
C
926
181
K
927
182
R
928
183
V
929
184
L
930
185
N
931
186
V
932
187
V
933
188
C
934
189
K
935
190
T
936
191
C
937
192
G
938
193
Q
939
194
Q
940
195
Q
941
196
T
942
197
T
943
198
L
944
199
K
945
200
G
946
201
V
947
202
E
948
203
A
949
204
V
950
205
M
951
206
Y
952
207
M
953
208
G
954
209
T
955
210
L
956
211
S
957
212
Y
958
213
E
959
214
Q
960
215
F
961
216
K
962
217
K
963
218
G
964
219
V
965
220
Q
966
221
I
967
222
P
968
223
C
971
226
G
972
227
K
973
228
Q
974
229
A
975
230
T
976
231
K
977
232
Y
978
233
L
979
234
V
980
235
Q
981
236
Q
982
237
E
983
238
S
984
239
P
985
240
F
986
241
V
987
242
M
988
243
M
989
244
S
990
245
A
991
246
P
992
247
P
993
248
A
994
249
Q
995
250
Y
996
251
E
997
252
L
998
253
K
999
254
H
1000
255
G
1001
256
T
1002
257
F
1003
258
T
1004
259
C
1005
260
A
1006
261
S
1007
262
E
1008
263
Y
1009
264
T
1010
265
G
1011
266
N
1012
267
Y
1013
268
Q
1014
269
C
1015
270
G
1016
271
H
1017
272
Y
1018
273
K
1019
274
H
1020
275
I
1021
276
T
1022
277
S
1023
278
K
1024
279
E
1025
280
T
1026
281
L
1027
282
Y
1028
283
C
1029
284
I
1030
285
D
1031
286
G
1032
287
A
1033
288
L
1034
289
L
1035
290
T
1036
291
K
1037
292
S
1038
293
S
1039
294
E
1040
295
Y
1041
296
K
1042
297
G
1043
298
P
1044
299
I
1045
300
T
1046
301
D
1047
302
V
1048
303
F
1049
304
Y
1050
305
K
1051
306
E
1052
307
N
1053
308
S
1054
309
Y
1055
310
T
1056
311
T
1057
312
T
1058
313
I
1059
314
Impact score

Select a variant from the sequence above to obtain its impact score as well as mutation effect and time-dependent descriptors.