Project name: 4AJY_L184P [mutate: LP184V]

Status: done

Started: 2020-09-18 14:59:10
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 LP184V
Energy difference between WT (input) and mutated protein (by FoldX) 3.27122 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                                                       (00:01:39)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:52)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:39)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:44)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:45)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:46)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:46)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:47)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:48)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:49)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:49)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:50)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:50)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:51)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:52)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:53)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:26:00)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:26:00)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:26:00)
[INFO]       Main:     Simulation completed successfully.                                          (00:26:01)
Show buried residues

Minimal score value
-3.9314
Maximal score value
2.4009
Average score
-0.5586
Total score value
-82.6701

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 -2.3583
61 P V -1.3233
62 V V 0.0405
63 L V 1.2334
64 R V 0.3641
65 S V 0.4457
66 V V 0.4892
67 N V -0.5696
68 S V -1.4722
69 R V -2.4645
70 E V -2.0981
71 P V -1.6271
72 S V 0.0000
73 Q V -1.5591
74 V V 0.0000
75 I V -0.5457
76 F V 0.0000
77 C V -1.0767
78 N V 0.0000
79 R V -2.5027
80 S V -1.4623
81 P V 0.0000
82 R V -2.0784
83 V V -0.8000
84 V V 0.0000
85 L V 0.0000
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 L V 0.2210
90 N V 0.3599
91 F V 1.4317
92 D V -0.5074
93 G V -0.8583
94 E V -1.1081
95 P V -0.7140
96 Q V -0.9383
97 P V -0.5168
98 Y V -0.0749
99 P V -0.0976
100 T V -0.1499
101 L V 0.0000
102 P V -1.1306
103 P V -1.5810
104 G V -1.6826
105 T V -1.5268
106 G V -1.9946
107 R V -2.7458
108 R V -2.7078
109 I V 0.0000
110 H V -1.8707
111 S V 0.0000
112 Y V -0.9674
113 R V -0.9785
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 -0.1811
121 D V 0.0000
122 A V -0.6116
123 G V -0.5393
124 T V -0.2175
125 H V -0.7566
126 D V 0.0000
127 G V 0.3859
128 L V 0.0000
129 L V 1.2612
130 V V 0.0000
131 N V -1.4513
132 Q V -1.6020
133 T V -0.8896
134 E V 0.0000
135 L V 0.0000
136 F V 0.0000
137 V V 0.3932
138 P V 0.0000
139 S V 0.0000
140 L V 1.0843
141 N V -0.4308
142 V V 0.2724
143 D V -1.8829
144 G V -1.7336
145 Q V -1.1670
146 P V -0.2494
147 I V 0.9294
148 F V 1.5509
149 A V 0.0000
150 N V -0.7295
151 I V 0.0000
152 T V -0.2623
153 L V 0.0000
154 P V 0.9315
155 V V 2.4009
156 Y V 2.0366
157 T V 1.2529
158 L V 1.4192
159 K V -0.3156
160 E V 0.0000
161 R V 0.7515
162 C V 0.9167
163 L V 0.7837
164 Q V 0.0000
165 V V 1.1172
166 V V 1.1059
167 R V 0.0000
168 S V 0.7037
169 L V 1.3724
170 V V -0.3006
171 K V -2.3214
172 P V -2.4960
173 E V -3.7208
174 N V -3.0024
175 Y V 0.0000
176 R V -3.9314
177 R V -3.4100
178 L V -1.2173
179 D V -1.7018
180 I V -0.2551
181 V V 0.5880
182 R V -1.5310
183 S V -0.9049
184 P V 0.0000 mutated: LP184V
185 Y V -1.3299
186 E V -2.4250
187 D V -1.6360
188 L V 0.0000
189 E V -2.2586
190 D V 0.0000
191 H V -1.9964
192 P V 0.0000
193 N V -2.1107
194 V V -1.2851
195 Q V -2.1044
196 K V -2.6150
197 D V 0.0000
198 L V 0.0000
199 E V -2.4696
200 R V -2.0630
201 L V 0.0000
202 T V 0.0000
203 Q V -1.9140
204 E V -1.5254
205 R V -1.4479
206 I V 0.4937
207 A V 0.0761
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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, -0.5586 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_3 -0.5586 View CSV PDB
model_9 -0.5614 View CSV PDB
model_7 -0.6047 View CSV PDB
model_2 -0.615 View CSV PDB
model_1 -0.632 View CSV PDB
model_0 -0.6414 View CSV PDB
model_11 -0.6461 View CSV PDB
model_6 -0.663 View CSV PDB
model_8 -0.6729 View CSV PDB
model_5 -0.6768 View CSV PDB
model_10 -0.7668 View CSV PDB
input -0.7968 View CSV PDB
model_4 -0.8444 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018