Project name: 4AJY_L89P [mutate: LP89V]

Status: done

Started: 2020-09-18 14:57:02
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 LP89V
Energy difference between WT (input) and mutated protein (by FoldX) 4.51884 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                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:40)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:43)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:27)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:25:35)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:25:36)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:25:36)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:25:37)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:25:38)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:25:38)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:25:39)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:25:40)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:25:40)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:25:42)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:25:45)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:25:48)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:25:48)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:25:52)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:25:52)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:25:52)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:53)
Show buried residues
Minimal score value
-3.8749
Maximal score value
2.3515
Average score
-0.7744
Total score value
-114.6122
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 -2.5873
61 P V -1.5135
62 V V 0.0000
63 L V -0.4888
64 R V -1.1431
65 S V -0.5730
66 V V -0.6169
67 N V -1.6990
68 S V -1.8751
69 R V -3.0787
70 E V -3.6962
71 P V -2.5774
72 S V 0.0000
73 Q V -1.7505
74 V V 0.0000
75 I V 0.1641
76 F V 0.0000
77 C V -0.5495
78 N V 0.0000
79 R V -2.2339
80 S V -1.4557
81 P V 0.0000
82 R V -2.2018
83 V V 0.0000
84 V V 0.0000
85 L V 0.4136
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 P V 0.0000 mutated: LP89V
90 N V -0.8245
91 F V -0.2294
92 D V -1.9509
93 G V -2.0373
94 E V -1.9921
95 P V -1.4212
96 Q V -0.5740
97 P V -0.4033
98 Y V 0.3450
99 P V 0.0000
100 T V 0.2353
101 L V -0.1371
102 P V -0.9069
103 P V -1.5024
104 G V -1.6679
105 T V -1.1233
106 G V -1.2699
107 R V -1.4776
108 R V -2.0267
109 I V 0.0000
110 H V -1.9714
111 S V 0.0000
112 Y V 0.0000
113 R V -2.1934
114 G V -0.6730
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 -0.3771
123 G V -0.1936
124 T V 0.1626
125 H V -0.4260
126 D V 0.0000
127 G V 0.0000
128 L V 0.4647
129 L V 0.3755
130 V V 0.0000
131 N V -1.6468
132 Q V -2.0234
133 T V -1.4300
134 E V -2.1779
135 L V 0.0000
136 F V 0.0000
137 V V 0.2603
138 P V 0.3285
139 S V 0.7577
140 L V 1.0546
141 N V -0.3811
142 V V 0.3920
143 D V -1.6057
144 G V -1.5191
145 Q V 0.0000
146 P V -0.1008
147 I V 0.0000
148 F V 1.5091
149 A V 0.0000
150 N V -0.4108
151 I V 0.0000
152 T V -0.4716
153 L V 0.0000
154 P V 0.4111
155 V V 1.8626
156 Y V 1.0760
157 T V 0.4929
158 L V 0.8432
159 K V -1.1116
160 E V -0.4632
161 R V 0.3757
162 C V 0.9300
163 L V 0.0000
164 Q V 0.0000
165 V V 2.3515
166 V V 1.8456
167 R V 0.0000
168 S V 0.8936
169 L V 1.7065
170 V V -0.1519
171 K V -2.3886
172 P V -2.5012
173 E V -3.3826
174 N V -2.5904
175 Y V 0.0000
176 R V -3.3580
177 R V -2.8190
178 L V -0.6067
179 D V -1.5495
180 I V 0.3433
181 V V 0.1311
182 R V -1.7366
183 S V -1.6123
184 L V -1.0083
185 Y V -1.8971
186 E V -2.9713
187 D V -2.1131
188 L V 0.0000
189 E V -2.6339
190 D V -2.3460
191 H V -2.0406
192 P V 0.0000
193 N V -1.7473
194 V V -1.3779
195 Q V -2.0211
196 K V -2.8618
197 D V -2.3832
198 L V 0.0000
199 E V -3.5715
200 R V -3.8749
201 L V 0.0000
202 T V -2.9584
203 Q V -2.8938
204 E V -3.3784
205 R V -2.6852
206 I V 0.1060
207 A V -0.2223
Download PDB file
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, -0.7744 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_8 -0.7744 View CSV PDB
input -0.7934 View CSV PDB
model_9 -0.8195 View CSV PDB
model_4 -0.8351 View CSV PDB
model_3 -0.8535 View CSV PDB
model_5 -0.8906 View CSV PDB
model_0 -0.8974 View CSV PDB
model_2 -0.9046 View CSV PDB
model_10 -0.9065 View CSV PDB
model_7 -0.9154 View CSV PDB
model_1 -0.9222 View CSV PDB
model_11 -0.9562 View CSV PDB
model_6 -0.9723 View CSV PDB
 
Laboratory of Theory of Biopolymers 2018