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Simulation report and files

General information

Name: Spike protein bound to the human ACE2 receptor

Included proteins: ACE2, Spike

Uniprot ID: Q9BYF1

Species: Homo sapiens (Human)

PDB ID: 6M0J

Submitted by: California State University, Los Angeles and Virginia Tech

Submission date: October 31, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: TIP3P

Total number of atoms: 117028

Simulation details

Software and version: Amber18 Pmem Cuda N/D

Forcefield and version: Amber ff14SB N/D

Time step : 2.0 fs

Delta : 0.02 ns

Replicates: 1

Accumulated simulation time: 0.0500 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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Spike protein bound to the human ACE2 receptor ( 6M0J)

Selection

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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
Spike
AA
Seq. pos.
PDB resID
T
333
257
N
334
258
L
335
262
V
336
264
P
337
265
F
338
266
G
339
267
E(Q)
340
268
V(K)
341
269
F(P)
342
270
N
343
271
A(V)
344
274
T
345
275
R(D)
346
276
A
348
277
S(M)
349
278
V
350
279
Y(Q)
351
281
A
352
282
W
353
283
N(D)
354
284
R(A)
355
285
K(Q)
356
286
R
357
287
I
358
288
S(F)
359
289
N(K)
360
290
C(E)
361
291
A
363
292
D(F)
364
296
Y(V)
365
297
S
366
298
V
367
299
L
368
301
Y(P)
369
302
N
370
303
S(T)
371
305
A(Q)
372
306
S(G)
373
307
F
374
308
S
375
312
T
376
315
F(Q)
377
321
K
378
322
C(A)
379
323
V
382
324
S(H)
383
326
P
384
327
T
385
328
K(A)
386
329
L(W)
387
330
D
389
331
L
390
332
C(G)
391
333
F(K)
392
334
T(G)
393
335
D
398
336
F
400
337
V(R)
401
338
R
403
339
G
404
340
D
405
341
E
406
342
V
407
343
R
408
344
Q
409
345
I
410
346
A
411
347
P
412
348
G
413
349
Q
414
350
T
415
351
G
416
352
K
417
353
I
418
354
A
419
355
D
420
356
Y
421
357
N
422
358
Y
423
359
K
424
360
L
425
361
P
426
362
D
427
363
D
428
364
F
429
365
T
430
366
G
431
367
C
432
368
V
433
369
I
434
370
A
435
371
W
436
372
N
437
373
S
438
374
N
439
375
N
440
376
L
441
377
D
442
378
S
443
379
K
444
380
V
445
381
G
446
382
G
447
383
N
448
384
Y
449
385
N
450
386
Y
451
387
L
452
388
Y
453
389
R
454
390
L
455
391
F
456
392
R
457
393
K
458
394
S
459
395
N
460
396
L
461
397
K
462
398
P
463
399
F
464
400
E
465
401
R
466
402
D
467
403
I
468
404
S
469
405
T
470
406
E
471
407
I
472
408
Y
473
409
Q
474
410
A
475
411
G
476
412
S
477
413
T
478
414
P
479
415
C
480
416
N
481
417
G
482
418
V
483
419
E
484
420
G
485
421
F
486
422
N
487
423
C
488
424
Y
489
425
F
490
426
P
491
427
L
492
428
Q
493
429
S
494
430
Y
495
431
G
496
432
F
497
433
Q
498
434
P
499
435
T
500
436
N
501
437
G
502
438
V
503
439
G
504
440
Y
505
441
Q
506
442
P
507
443
Y
508
444
R
509
445
V
510
446
V
511
447
V
512
448
L
513
449
S
514
450
F
515
451
E
516
452
L
517
453
L
518
454
H
519
455
A
520
456
P
521
457
A
522
458
T
523
459
V
524
460
C
525
461
G
526
462
Impact score

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