Project name: 4AJY_V74D [mutate: VD74V]

Status: done

Started: 2020-09-18 15:00:56
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA
input PDB
Selected Chain(s) V
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues VD74V
Energy difference between WT (input) and mutated protein (by FoldX) 5.55366 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with V chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:00)
[INFO]       FoldX:    Building mutant model                                                       (00:01:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:40)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:29)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:24:43)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:24:43)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:24:44)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:24:45)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:24:45)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:24:46)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:24:47)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:24:47)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:24:48)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:24:48)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:24:49)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:24:50)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:24:50)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:24:51)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:24:52)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:24:52)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:53)
Show buried residues

Minimal score value
-3.9269
Maximal score value
1.8437
Average score
-0.7512
Total score value
-111.1722

The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan3D score mutation
residue index residue name chain Aggrescan3D score
mutation
60 R V -1.8529
61 P V -0.8521
62 V V 0.2024
63 L V 0.7669
64 R V 0.2430
65 S V 0.7475
66 V V 0.7148
67 N V -0.6746
68 S V -1.4839
69 R V -2.6379
70 E V -2.9011
71 P V -1.9731
72 S V 0.0000
73 Q V -1.3768
74 D V 0.0000 mutated: VD74V
75 I V -0.5379
76 F V 0.0000
77 C V -1.1325
78 N V 0.0000
79 R V -2.2787
80 S V -1.3215
81 P V -1.0303
82 R V -1.1773
83 V V -0.2174
84 V V 0.0000
85 L V 0.4329
86 P V 0.0000
87 V V 0.0000
88 W V 0.0526
89 L V 0.0000
90 N V 0.0000
91 F V -0.2853
92 D V -1.9284
93 G V -1.9003
94 E V -2.3709
95 P V -1.5199
96 Q V -0.7602
97 P V -0.3568
98 Y V 0.4010
99 P V 0.0665
100 T V 0.1503
101 L V 0.0000
102 P V -0.8206
103 P V -1.0377
104 G V -1.2772
105 T V -1.5544
106 G V -2.0226
107 R V -2.9317
108 R V -2.6450
109 I V 0.0000
110 H V -1.9404
111 S V 0.0000
112 Y V -1.1556
113 R V -1.1564
114 G V 0.0000
115 H V 0.0000
116 L V 0.0000
117 W V 0.0000
118 L V 0.0000
119 F V 0.0000
120 R V -0.6444
121 D V 0.0000
122 A V -0.2791
123 G V -0.3074
124 T V 0.0000
125 H V -0.6050
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V -0.2522
130 V V 0.0000
131 N V -1.3715
132 Q V -1.7426
133 T V -1.0898
134 E V -1.0412
135 L V 0.0000
136 F V 0.0000
137 V V 1.3968
138 P V 0.0000
139 S V 0.2432
140 L V 0.2485
141 N V -1.4279
142 V V -1.5924
143 D V -2.5791
144 G V -1.8804
145 Q V -1.3358
146 P V -0.4875
147 I V 1.0408
148 F V 1.8437
149 A V 0.0000
150 N V 0.0000
151 I V 0.0000
152 T V 0.0000
153 L V 0.0000
154 P V 0.2819
155 V V 0.6317
156 Y V 1.4130
157 T V 0.6615
158 L V 0.7984
159 K V -0.9750
160 E V -0.4209
161 R V -0.4554
162 C V 0.2301
163 L V 0.0000
164 Q V 0.0298
165 V V 0.8733
166 V V 0.8783
167 R V -0.1621
168 S V 0.3247
169 L V 1.2676
170 V V -0.3172
171 K V -2.3901
172 P V -2.8261
173 E V -3.6378
174 N V -3.1836
175 Y V 0.0000
176 R V -3.9269
177 R V -2.8399
178 L V -0.8305
179 D V -0.9002
180 I V 1.2647
181 V V 1.1871
182 R V -1.4003
183 S V -1.2940
184 L V -1.0934
185 Y V -2.0635
186 E V -3.3294
187 D V -2.3676
188 L V 0.0000
189 E V -3.4609
190 D V -2.5909
191 H V 0.0000
192 P V -1.6432
193 N V -1.8196
194 V V 0.0000
195 Q V -2.2056
196 K V -2.3673
197 D V -1.8680
198 L V 0.0000
199 E V -2.6180
200 R V -2.9257
201 L V 0.0000
202 T V -1.9247
203 Q V -2.5654
204 E V -3.1537
205 R V -2.3699
206 I V -0.0145
207 A V 0.1238
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CABS-flex predictions of flexibility of input structure

In dynamic mode, A3D analysis is performed on the set of models reflecting fluctuations of the input structure (predicted by CABS-flex method, models are numbered from 0 to 11) and the input model. Their A3D scores are provided below in the table.
The right panel presents comparison of the most aggregation prone model (with the highest A3D score, -0.7512 in this case) with the input model (the most aggregation prone model in blue, input in red) and RMSF plot which shows the extent of residue fluctuations in Angstroms (predicted by CABS-flex).

Model
Average A3D Score
model_1 -0.7512 View CSV PDB
model_11 -0.7533 View CSV PDB
input -0.79 View CSV PDB
model_6 -0.8142 View CSV PDB
model_10 -0.8505 View CSV PDB
model_2 -0.8586 View CSV PDB
model_7 -0.8599 View CSV PDB
model_4 -0.8855 View CSV PDB
model_3 -0.9142 View CSV PDB
model_9 -0.9196 View CSV PDB
model_0 -0.9634 View CSV PDB
model_8 -0.9898 View CSV PDB
model_5 -1.0079 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018