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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.

Viewer

PL-PRO ( 6W9C)

Selection

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Relevant domains

Active site

Repeat

Zinc finger region

Domain of interest

Custom selection
Input your selection using the NGL selection language.

Toolkit

General
Interaction network

Hydrogen bonds

  • Interacting pairs
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  • Simulation
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  • Summary
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.

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

Please select a variant from the sequence above.
All contacts
0
0

Please select a variant from the sequence above.
Hydrogen bond contacts
0
0

Please select a variant from the sequence above.
Salt bridge contacts
0
0

Please select a variant from the sequence above.
Hydrophobic contacts
0
0

Please select a variant from the sequence above.
Pi-cation contacts
0
0

Please select a variant from the sequence above.
Pi-stacking contacts
0
0

Please select a variant from the sequence above.
T-stacking contacts
0
0

Please select a variant from the sequence above.
Van der Waals contacts
0
0

Please select a variant from the sequence above.
Water bridge contacts
0
0

Please select a variant from the sequence above.
Extended water bridge contacts
0
0

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User-provided descriptors 0/0

Upload your own descriptors according to this template.