Project name: 4AJY_Y112D [mutate: YD112V]

Status: done

Started: 2020-09-18 15:03:21
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 YD112V
Energy difference between WT (input) and mutated protein (by FoldX) 3.02132 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
Downloads Download all the data
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                                                       (00:01:41)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:46)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:41)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:18)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:19)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:19)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:20)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:20)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:21)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:21)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:22)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:23)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:23)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:24)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:24)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:25)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:25:26)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:25:26)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:25:26)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:27)
Show buried residues
Minimal score value
-3.947
Maximal score value
1.5365
Average score
-0.8077
Total score value
-119.5406
Download the table (csv)

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 -1.9213
61 P V -1.1993
62 V V -0.4089
63 L V 0.7907
64 R V -0.3095
65 S V 0.0000
66 V V 0.3349
67 N V -1.5496
68 S V -1.5663
69 R V -2.9195
70 E V -3.0015
71 P V -2.5814
72 S V 0.0000
73 Q V -1.3998
74 V V 0.0000
75 I V -0.1116
76 F V 0.0000
77 C V -0.5931
78 N V 0.0000
79 R V -2.1439
80 S V -1.2111
81 P V -1.0468
82 R V -0.8830
83 V V -0.0765
84 V V 0.0000
85 L V 0.3728
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 L V 0.0000
90 N V 0.0000
91 F V 0.0035
92 D V -1.5198
93 G V -1.3599
94 E V -2.1466
95 P V -1.1569
96 Q V -0.7396
97 P V -0.3020
98 Y V 0.0747
99 P V -0.0211
100 T V 0.5984
101 L V 0.8071
102 P V -0.2714
103 P V -0.4357
104 G V -1.0535
105 T V -0.7604
106 G V -1.0460
107 R V -1.6926
108 R V -2.0437
109 I V 0.0000
110 H V -1.1173
111 S V 0.0000
112 D V 0.0000 mutated: YD112V
113 R V -1.6942
114 G V -1.1550
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 -0.3936
121 D V 0.0000
122 A V -0.1857
123 G V -0.3394
124 T V 0.0000
125 H V -0.6156
126 D V 0.0000
127 G V -0.1216
128 L V 0.0000
129 L V 0.3508
130 V V 0.0000
131 N V -1.2463
132 Q V -1.0344
133 T V -0.3336
134 E V 0.0000
135 L V 0.0000
136 F V -0.0391
137 V V 0.5313
138 P V 0.0000
139 S V -0.0498
140 L V -0.3457
141 N V -2.1412
142 V V 0.0000
143 D V -2.7087
144 G V -1.9597
145 Q V -1.4371
146 P V -0.5964
147 I V 0.8548
148 F V 1.5365
149 A V 0.0000
150 N V -1.1922
151 I V 0.0000
152 T V -0.6273
153 L V 0.0000
154 P V 0.3090
155 V V 0.7693
156 Y V 1.4868
157 T V 0.5838
158 L V 0.8708
159 K V -1.2005
160 E V -1.2145
161 R V -0.2363
162 C V 0.3528
163 L V 0.2558
164 Q V 0.0000
165 V V 0.5018
166 V V 0.9876
167 R V 0.0000
168 S V 0.1788
169 L V 1.3531
170 V V 0.1715
171 K V -2.2572
172 P V -2.2808
173 E V -3.5506
174 N V -2.5526
175 Y V 0.0000
176 R V -3.9470
177 R V -3.0882
178 L V -0.9999
179 D V -1.2940
180 I V 0.8305
181 V V 0.3250
182 R V -2.0466
183 S V -1.4407
184 L V -0.9735
185 Y V -2.1430
186 E V -3.6158
187 D V -3.4745
188 L V 0.0000
189 E V -3.4503
190 D V -3.4065
191 H V -2.3084
192 P V -2.1674
193 N V -2.0182
194 V V -1.6518
195 Q V -2.5594
196 K V -2.7757
197 D V -2.4373
198 L V -2.5587
199 E V -3.3404
200 R V -3.4339
201 L V -2.1749
202 T V 0.0000
203 Q V -2.6724
204 E V -2.6070
205 R V -2.0139
206 I V -0.0971
207 A V 0.0225
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View in 3Dmol
Play the video

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, -0.8077 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_4 -0.8077 View CSV PDB
input -0.8097 View CSV PDB
model_1 -0.8972 View CSV PDB
model_0 -0.9164 View CSV PDB
model_7 -0.9302 View CSV PDB
model_3 -0.9332 View CSV PDB
model_6 -0.9689 View CSV PDB
model_5 -0.9695 View CSV PDB
model_2 -0.9753 View CSV PDB
model_8 -0.9806 View CSV PDB
model_9 -0.9961 View CSV PDB
model_10 -1.0028 View CSV PDB
model_11 -1.0049 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018