Project name: 1LM8_S65W [mutate: SW65V]

Status: done

Started: 2020-09-20 09:33:13
Settings
Chain sequence(s) V: RPVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQ
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) 72.737 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure

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Simulation log
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with V chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:37)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:01:46)
[INFO]       CABS:     Running CABS flex simulation                                                (00:02:38)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:21:11)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:21:11)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:21:12)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:21:13)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:21:13)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:21:14)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:21:15)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:21:15)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:21:16)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:21:16)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:21:17)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:21:18)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:21:18)
[WARNING]    CABS:     Pymol failed to launch (most likely not present on the system).Couldn't     
                       create a superimposed picture of CABS input and output                      (00:21:20)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:21:20)
[CRITICAL]   pyMol:    Pymol encountered an error: /bin/sh: pymol: command not found Movie         
                       creation failed.                                                            (00:21:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:21:21)
Show buried residues

Minimal score value
-4.4579
Maximal score value
1.7682
Average score
-0.7056
Total score value
-105.8388

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 -2.6037
61 P V -2.3726
62 V V 0.0000
63 L V -0.9594
64 R V -0.4001
65 W V 1.2034 mutated: SW65V
66 V V 1.3281
67 N V -0.5934
68 S V -1.2509
69 R V -2.3494
70 E V -2.2298
71 P V -2.0237
72 S V 0.0000
73 Q V 0.0000
74 V V 0.0000
75 I V -0.0942
76 F V 0.0000
77 C V -0.9160
78 N V 0.0000
79 R V -2.3241
80 S V -1.3008
81 P V -1.2139
82 R V -1.9527
83 V V -0.9065
84 V V 0.0000
85 L V 0.0899
86 P V 0.0000
87 V V 0.0000
88 W V 0.0000
89 L V 0.0000
90 N V 0.0901
91 F V 0.3856
92 D V -1.7158
93 G V -1.9011
94 E V -2.3699
95 P V -1.4660
96 Q V -0.8139
97 P V -0.5283
98 Y V 0.1798
99 P V 0.0793
100 T V 0.1367
101 L V 0.3079
102 P V -0.5715
103 P V -1.4101
104 G V -1.4704
105 T V -0.9792
106 G V -1.1154
107 R V -1.1769
108 R V -1.8904
109 I V 0.0000
110 H V -1.6661
111 S V 0.0000
112 Y V -0.8968
113 R V -1.4949
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 -0.2858
121 D V 0.0000
122 A V -0.5511
123 G V -0.5601
124 T V -0.8963
125 H V -0.7069
126 D V 0.0000
127 G V 0.0000
128 L V 0.0000
129 L V -0.3670
130 V V -0.8470
131 N V -1.9249
132 Q V -1.8291
133 T V 0.0000
134 E V -1.4618
135 L V -0.0558
136 F V 0.3067
137 V V 0.7543
138 P V 0.0000
139 S V -0.4526
140 L V -0.9320
141 N V -2.2544
142 V V -2.0788
143 D V -2.7974
144 G V -2.1410
145 Q V -2.0488
146 P V -0.7708
147 I V 0.7191
148 F V 1.7010
149 A V 0.0000
150 N V -0.9785
151 I V 0.0000
152 T V -0.6086
153 L V 0.0000
154 P V 0.0454
155 V V 1.7214
156 Y V 0.9012
157 T V 0.5237
158 L V 0.8723
159 K V -0.7017
160 E V 0.0000
161 R V 0.2291
162 C V 0.8065
163 L V 0.0000
164 Q V 0.4485
165 V V 1.7682
166 V V 1.6679
167 R V 0.0000
168 S V 0.4593
169 L V 1.5593
170 V V 0.0562
171 K V -1.8215
172 P V -2.3817
173 E V -3.2200
174 N V -2.6365
175 Y V 0.0000
176 R V -4.4579
177 R V -3.1558
178 L V -1.0525
179 D V -2.3229
180 I V -0.2272
181 V V 0.8041
182 R V -1.7024
183 S V -0.9289
184 L V 0.2071
185 Y V -1.4013
186 E V -2.5102
187 D V -1.8223
188 L V 0.0000
189 E V -3.1910
190 D V -2.6209
191 H V -1.6655
192 P V 0.0000
193 N V -1.2407
194 V V 0.0000
195 Q V -2.0509
196 K V -2.2447
197 D V 0.0000
198 L V 0.0000
199 E V -2.6109
200 R V -2.4200
201 L V 0.0000
202 T V 0.0000
203 Q V -1.7066
204 E V -1.5581
205 R V -1.2634
206 I V 0.4899
207 A V -0.3479
208 H V -1.4179
209 Q V -1.4929
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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, -0.7056 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 -0.7056 View CSV PDB
model_0 -0.7831 View CSV PDB
model_6 -0.8119 View CSV PDB
model_9 -0.828 View CSV PDB
model_10 -0.8451 View CSV PDB
model_7 -0.87 View CSV PDB
model_1 -0.8776 View CSV PDB
model_2 -0.8816 View CSV PDB
model_3 -0.9137 View CSV PDB
model_5 -0.921 View CSV PDB
model_11 -0.9247 View CSV PDB
input -0.945 View CSV PDB
model_4 -1.0313 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018