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General information

Name: Nucleocapsid dimerization domain P21 form in aqueous solution

Included proteins: N

Uniprot ID: P0DTC9

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

PDB ID: 6WZQ

Submitted by: Institut Hospital del Mar d'Investigacions Mèdiques

Submission date: February 16, 2021

System setup

Ligands: None

Membrane composition: None

Solvent type: TIP3P

Total number of atoms: 44268

Simulation details

Software and version: AceMD 3.2.3

Forcefield and version: CHARMM36 2019

Time step : 4.0 fs

Delta : 0.1 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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Nucleocapsid dimerization domain P21 form in aqueous solution ( 6WZQ)

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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
N
AA
Seq. pos.
PDB resID
A
251
251
A
252
252
E
253
253
A
254
254
S
255
255
K
256
256
K
257
257
P
258
258
R
259
259
Q
260
260
K
261
261
R
262
262
T
263
263
A
264
264
T
265
265
K
266
266
A
267
267
Y
268
268
N
269
269
V
270
270
T
271
271
Q
272
272
A
273
273
F
274
274
G
275
275
R
276
276
R
277
277
G
278
278
P
279
279
E
280
280
Q
281
281
T
282
282
Q
283
283
G
284
284
N
285
285
F
286
286
G
287
287
D
288
288
Q
289
289
E
290
290
L
291
291
I
292
292
R
293
293
Q
294
294
G
295
295
T
296
296
D
297
297
Y
298
298
K
299
299
H
300
300
W
301
301
P
302
302
Q
303
303
I
304
304
A
305
305
Q
306
306
F
307
307
A
308
308
P
309
309
S
310
310
A
311
311
S
312
312
A
313
313
F
314
314
F
315
315
G
316
316
M
317
317
S
318
318
R
319
319
I
320
320
G
321
321
M
322
322
E
323
323
V
324
324
T
325
325
P
326
326
S
327
327
G
328
328
T
329
329
W
330
330
L
331
331
T
332
332
Y
333
333
T
334
334
G
335
335
A
336
336
I
337
337
K
338
338
L
339
339
D
340
340
D
341
341
K
342
342
D
343
343
P
344
344
N
345
345
F
346
346
K
347
347
D
348
348
Q
349
349
V
350
350
I
351
351
L
352
352
L
353
353
N
354
354
K
355
355
H
356
356
I
357
357
D
358
358
A
359
359
Y
360
360
K
361
361
T
362
362
F
363
363
P
364
364
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

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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

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