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General information

Name: NSP1 in aqueous solution

Included proteins: NSP1

Uniprot ID: P0DTD1

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

PDB ID: 7k3n

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: 21343

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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NSP1 in aqueous solution ( 7k3n)

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Interaction network

Hydrogen bonds

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RMSD
Trajectory:
Frames:
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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
NSP1
AA
Seq. pos.
PDB resID
V
14
5
Q
15
6
L
16
7
S
17
8
L
18
9
P
19
10
V
20
11
L
21
12
Q
22
13
V
23
14
R
24
15
D
25
16
V
26
17
L
27
18
V
28
19
R
29
20
G
30
21
F
31
22
G
32
23
D
33
24
S
34
25
V
35
26
E
36
27
E
37
28
V
38
29
L
39
30
S
40
31
E
41
32
A
42
33
R
43
34
Q
44
35
H
45
36
L
46
37
K
47
38
D
48
39
G
49
40
T
50
41
C
51
42
G
52
43
L
53
44
V
54
45
E
55
46
V
56
47
E
57
48
K
58
49
G
59
50
V
60
51
L
61
52
P
62
53
Q
63
54
L
64
55
E
65
56
Q
66
57
P
67
58
Y
68
59
V
69
60
F
70
61
I
71
62
K
72
63
R
73
64
S
74
65
D
75
66
G
82
73
H
83
74
V
84
75
M
85
76
V
86
77
E
87
78
L
88
79
V
89
80
A
90
81
E
91
82
L
92
83
E
93
84
G
94
85
I
95
86
Q
96
87
Y
97
88
G
98
89
R
99
90
S
100
91
G
101
92
E
102
93
T
103
94
L
104
95
G
105
96
V
106
97
L
107
98
V
108
99
P
109
100
H
110
101
V
111
102
G
112
103
E
113
104
I
114
105
P
115
106
V
116
107
A
117
108
Y
118
109
R
119
110
K
120
111
V
121
112
L
122
113
L
123
114
R
124
115
K
125
116
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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