Project name: 4AJY_S65W2 [mutate: SW65V]

Status: done

Started: 2020-09-20 09:50:55
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 SW65V
Energy difference between WT (input) and mutated protein (by FoldX) 75.7857 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                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:37)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:44)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:41)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:04)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:05)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:06)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:06)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:07)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:07)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:08)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:09)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:09)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:10)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:11)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:11)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:12)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:21:13)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:14)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:21:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:15)
Show buried residues

Minimal score value
-4.4056
Maximal score value
1.9966
Average score
-0.7571
Total score value
-112.0506

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 -2.2402
61 P V -0.5781
62 V V 1.3311
63 L V 0.0000
64 R V 0.0780
65 W V 1.4446 mutated: SW65V
66 V V 1.9966
67 N V 0.0000
68 S V -1.2062
69 R V -2.5592
70 E V -2.6964
71 P V -2.3984
72 S V 0.0000
73 Q V -1.9049
74 V V 0.0000
75 I V -0.4811
76 F V 0.0000
77 C V -1.1317
78 N V -1.6111
79 R V -2.3402
80 S V -1.2279
81 P V -0.7572
82 R V -0.2543
83 V V 0.8118
84 V V 0.0000
85 L V 1.0883
86 P V 0.0000
87 V V 0.2259
88 W V 0.0000
89 L V 0.2174
90 N V 0.0000
91 F V 1.8105
92 D V -0.1605
93 G V -0.6057
94 E V -0.7645
95 P V -0.6889
96 Q V -1.1952
97 P V -0.5532
98 Y V -0.1446
99 P V -0.2127
100 T V 0.4444
101 L V -0.0319
102 P V -0.4488
103 P V -1.0577
104 G V -1.7306
105 T V -1.4663
106 G V -1.6294
107 R V -2.1292
108 R V -2.4329
109 I V 0.0000
110 H V -1.6128
111 S V 0.0000
112 Y V -1.0243
113 R V -0.8670
114 G V 0.0289
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 0.0000
121 D V 0.0000
122 A V 0.2623
123 G V -0.3058
124 T V -0.1877
125 H V 0.0000
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V -0.0946
130 V V 0.0000
131 N V -0.7730
132 Q V -1.3512
133 T V -0.3997
134 E V 0.0000
135 L V 0.2184
136 F V 0.0000
137 V V 1.8914
138 P V 0.0000
139 S V 0.1070
140 L V -1.0387
141 N V -2.3846
142 V V 0.0000
143 D V -3.0756
144 G V -2.1989
145 Q V -2.0705
146 P V -1.0488
147 I V 0.4511
148 F V 1.0367
149 A V 0.0000
150 N V -1.0517
151 I V 0.0000
152 T V -0.9717
153 L V 0.0000
154 P V 0.3166
155 V V 0.4574
156 Y V 0.5474
157 T V 0.3023
158 L V 0.7158
159 K V -0.4998
160 E V -0.4510
161 R V -0.5458
162 C V 0.0551
163 L V 0.0000
164 Q V 0.0000
165 V V 0.9097
166 V V 0.0000
167 R V -0.5431
168 S V 0.3833
169 L V 1.0897
170 V V -0.8068
171 K V -2.7703
172 P V -2.9376
173 E V -3.9039
174 N V -3.2395
175 Y V 0.0000
176 R V -4.4056
177 R V -3.4686
178 L V -1.4871
179 D V -2.2615
180 I V -0.1598
181 V V 0.2997
182 R V -1.8370
183 S V -1.4759
184 L V 0.0000
185 Y V -2.5832
186 E V -3.0274
187 D V -2.0853
188 L V 0.0000
189 E V -3.2183
190 D V -2.4609
191 H V -1.7353
192 P V -1.1750
193 N V -1.5609
194 V V -0.7406
195 Q V -2.0425
196 K V -2.4670
197 D V 0.0000
198 L V -2.2046
199 E V -4.1383
200 R V -4.0072
201 L V 0.0000
202 T V 0.0000
203 Q V -3.3140
204 E V -3.0854
205 R V -2.4864
206 I V -0.1504
207 A V -0.2004
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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, -0.7571 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_0 -0.7571 View CSV PDB
model_3 -0.7612 View CSV PDB
input -0.783 View CSV PDB
model_8 -0.796 View CSV PDB
model_2 -0.8264 View CSV PDB
model_6 -0.8472 View CSV PDB
model_1 -0.8572 View CSV PDB
model_5 -0.8623 View CSV PDB
model_10 -0.9021 View CSV PDB
model_9 -0.9163 View CSV PDB
model_11 -0.9561 View CSV PDB
model_4 -0.9887 View CSV PDB
model_7 -1.0206 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018