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Simulation report and files

General information

Name: NSP3

Included proteins: NSP3

Uniprot ID: P0DTD1

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

PDB ID: 6W02

Submitted by: Exscalate4CoV

Submission date: September 23, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 2506

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: 7.9995 µs

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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NSP3 ( 6W02)

Selection

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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
N
208
4
S
209
5
F
210
6
S
211
7
G
212
8
Y
213
9
L
214
10
K
215
11
L
216
12
T
217
13
D
218
14
N
219
15
V
220
16
Y
221
17
I
222
18
K
223
19
N
224
20
A
225
21
D
226
22
I
227
23
V
228
24
E
229
25
E
230
26
A
231
27
K
232
28
K
233
29
V
234
30
K
235
31
P
236
32
T
237
33
V
238
34
V
239
35
V
240
36
N
241
37
A
242
38
A
243
39
N
244
40
V
245
41
Y
246
42
L
247
43
K
248
44
H
249
45
G
250
46
G
251
47
G
252
48
V
253
49
A
254
50
G
255
51
A
256
52
L
257
53
N
258
54
K
259
55
A
260
56
T
261
57
N
262
58
N
263
59
A
264
60
M
265
61
Q
266
62
V
267
63
E
268
64
S
269
65
D
270
66
D
271
67
Y
272
68
I
273
69
A
274
70
T
275
71
N
276
72
G
277
73
P
278
74
L
279
75
K
280
76
V
281
77
G
282
78
G
283
79
S
284
80
C
285
81
V
286
82
L
287
83
S
288
84
G
289
85
H
290
86
N
291
87
L
292
88
A
293
89
K
294
90
H
295
91
C
296
92
L
297
93
H
298
94
V
299
95
V
300
96
G
301
97
P
302
98
N
303
99
V
304
100
N
305
101
K
306
102
G
307
103
E
308
104
D
309
105
I
310
106
Q
311
107
L
312
108
L
313
109
K
314
110
S
315
111
A
316
112
Y
317
113
E
318
114
N
319
115
F
320
116
N
321
117
Q
322
118
H
323
119
E
324
120
V
325
121
L
326
122
L
327
123
A
328
124
P
329
125
L
330
126
L
331
127
S
332
128
A
333
129
G
334
130
I
335
131
F
336
132
G
337
133
A
338
134
D
339
135
P
340
136
I
341
137
H
342
138
S
343
139
L
344
140
R
345
141
V
346
142
C
347
143
V
348
144
D
349
145
T
350
146
V
351
147
R
352
148
T
353
149
N
354
150
V
355
151
Y
356
152
L
357
153
A
358
154
V
359
155
F
360
156
D
361
157
K
362
158
N
363
159
L
364
160
Y
365
161
D
366
162
K
367
163
L
368
164
V
369
165
S
370
166
S
371
167
F
372
168
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.