Free cookie consent management tool by TermsFeed SCoV2-MD

Workbench

Simulation report and files

General information

Name: NSP9

Included proteins: NSP9

Uniprot ID: P0DTD1

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

PDB ID: 6W4B

Submitted by: Exscalate4CoV

Submission date: September 23, 2020

System setup

Ligands: None

Membrane composition: None

Solvent type: None

Total number of atoms: 3477

Simulation details

Software and version: GROMACS 2020

Forcefield and version: AMBER 99

Delta : 0.2 ns

Replicates: 1

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

NSP9 ( 6W4B)

Selection

Quick selection
Relevant domains

Site of interest

Custom selection
Input your selection using the NGL selection language.

Toolkit

General
Interaction network

Hydrogen bonds

  • Interacting pairs
  • Hide neighbours
  • All
  • Simulation
  • Current frame
  • 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
NSP9
AA
Seq. pos.
PDB resID
N
1
2
N
2
3
E
3
4
L
4
5
S
5
6
P
6
7
V
7
8
A
8
9
L
9
10
R
10
11
Q
11
12
M
12
13
S
13
14
C
14
15
A
15
16
A
16
17
G
17
18
T
18
19
T
19
20
Q
20
21
T
21
22
A
22
23
C
23
24
T
24
25
D
25
26
D
26
27
N
27
28
A
28
29
L
29
30
A
30
31
Y
31
32
Y
32
33
N
33
34
T
34
35
T
35
36
K
36
37
G
37
38
G
38
39
R
39
40
F
40
41
V
41
42
L
42
43
A
43
44
L
44
45
L
45
46
S
46
47
D
47
48
L
48
49
Q
49
50
D
50
51
L
51
52
K
52
53
W
53
54
A
54
55
R
55
56
F
56
57
P
57
58
K
58
59
S
59
60
D
60
61
G
61
62
T
62
63
G
63
64
T
64
65
I
65
66
Y
66
67
T
67
68
E
68
69
L
69
70
E
70
71
P
71
72
P
72
73
C
73
74
R
74
75
F
75
76
V
76
77
T
77
78
D
78
79
T
79
80
P
80
81
K
81
82
G
82
83
P
83
84
K
84
85
V
85
86
K
86
87
Y
87
88
L
88
89
Y
89
90
F
90
91
I
91
92
K
92
93
G
93
94
L
94
95
N
95
96
N
96
97
L
97
98
N
98
99
R
99
100
G
100
101
M
101
102
V
102
103
L
103
104
G
104
105
S
105
106
L
106
107
A
107
108
A
108
109
T
109
110
V
110
111
R
111
112
L
112
113
Impact score

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