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General information

Name: Main Protease (Mpro) in Complex with ML188 (A191V mutation)

Included proteins: NSP5

Uniprot ID: P0DTD1

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

PDB ID: 7L0D

Submitted by: Institut Hospital del Mar d'Investigacions Mèdiques

Submission date: March 04, 2021

System setup

Ligands:

ML188 (Orthosteric)

Membrane composition: None

Solvent type: TIP3P

Total number of atoms: 83402

Simulation details

Software and version: AceMD 3.2.3

Forcefield and version: CHARMM36 2019

Time step : 4.0 fs

Delta : 0.1 ns

Replicates: 3

Accumulated simulation time: 3.0000 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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Main Protease (Mpro) in Complex with ML188 (A191V mutation) ( 7L0D)

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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
NSP5
AA
Seq. pos.
PDB resID
S
1
1
G
2
2
F
3
3
R
4
4
K
5
5
M
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6
A
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F
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P
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S
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G
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K
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V
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E
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G
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C
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M
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V
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Q
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V
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T
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C
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G
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T
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T
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T
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L
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N
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G
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L
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W
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L
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D
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D
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V
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V
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Y
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C
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P
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R
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H
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V
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I
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C
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T
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S
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E
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D
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M
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L
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N
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P
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N
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Y
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E
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D
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L
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L
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I
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R
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K
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S
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N
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H
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N
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F
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L
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V
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Q
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A
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G
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N
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V
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Q
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L
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R
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V
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I
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G
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H
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S
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M
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Q
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N
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C
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V
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L
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K
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L
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K
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V
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D
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T
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A
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N
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P
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K
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T
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P
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K
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Y
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K
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F
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V
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R
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I
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Q
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P
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G
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Q
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T
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F
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S
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V
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114
L
115
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A
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C
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Y
118
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N
119
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G
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S
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P
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S
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G
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V
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Y
126
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Q
127
127
C
128
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A
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M
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R
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P
132
132
N
133
133
F
134
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T
135
135
I
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136
K
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G
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S
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F
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L
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N
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G
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S
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C
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G
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S
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V
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G
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F
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N
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I
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D
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Y
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154
D
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C
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V
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S
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F
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C
160
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Y
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M
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H
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H
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M
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E
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L
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P
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T
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G
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V
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H
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A
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G
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T
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D
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L
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E
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G
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N
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F
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Y
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G
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P
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F
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V
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D
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R
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Q
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T
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A(V)
191
191
Q
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A
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A
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G
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T
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D
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T
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T
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I
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T
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V
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N
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V
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L
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A
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W
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L
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Y
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A
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A
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V
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I
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N
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G
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D
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R
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W
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F
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L
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N
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R
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F
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T
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T
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T
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L
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N
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D
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F
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N
231
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L
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V
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A
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M
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K
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Y
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N
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Y
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E
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P
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L
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T
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Q
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D
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H
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D
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G
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P
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A
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Q
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T
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G
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I
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A
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V
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L
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D
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M
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C
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A
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S
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L
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K
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E
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L
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L
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Q
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273
N
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G
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M
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N
277
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G
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278
R
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T
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I
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281
L
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282
G
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283
S
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284
A
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285
L
286
286
L
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287
E
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288
D
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E
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F
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291
T
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P
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293
F
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D
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V
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V
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297
R
298
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Q
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299
C
300
300
S
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301
G
302
302
V
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303
T
304
304
F
305
305
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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