Project name: 6c82269e013b4af [mutate: GS74A]

Status: done

Started: 2020-04-05 14:03:31
Settings
Chain sequence(s) A: LTQPPSTSGTPGQRVTISCSGSSSNIETNTVNWYQQLPGTAPKLVMHTNNQRPSGVPDRFSGSRSGTSASLAIGGLQSEDEADYFCAAWDDNLNGVIFGGGTKLTVL
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
Dynamic mode Yes
Automated mutations No
Mutated residues GS74A
Energy difference between WT (input) and mutated protein (by FoldX) -0.00645566 kcal/mol
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 A 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                                                       (00:00:38)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:41)
[INFO]       CABS:     Running CABS flex simulation                                                (00:00:57)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:23:09)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:23:10)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:23:11)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:23:12)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:23:12)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:23:13)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:23:13)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:23:14)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:23:14)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:23:15)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:23:15)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:23:15)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:23:16)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:23:18)
[INFO]       Movie:    Creting movie with webm format                                              (00:25:02)
[INFO]       Main:     Simulation completed successfully.                                          (00:25:05)
Show buried residues

Minimal score value
-3.2289
Maximal score value
3.1834
Average score
-0.5283
Total score value
-56.5254

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
1 L A 1.8857
2 T A 0.5176
3 Q A 0.0000
4 P A -0.6503
5 P A -0.7971
6 S A -1.1284
7 T A -1.0017
8 S A -0.9565
9 G A 0.0000
10 T A -0.4869
11 P A -0.7742
12 G A -1.3647
13 Q A -2.1840
14 R A -2.5989
15 V A 0.0000
16 T A -0.7593
17 I A 0.0000
18 S A -0.2514
19 C A 0.0000
20 S A 0.0928
21 G A 0.4723
22 S A 0.0596
23 S A -0.2023
24 S A -0.4969
25 N A -0.7721
26 I A 0.2888
27 E A -1.4236
28 T A -1.3084
29 N A 0.0000
30 T A 0.0000
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A 0.8837
35 Q A 0.0000
36 Q A -0.9317
37 L A 0.0000
38 P A -1.3991
39 G A -0.8884
40 T A -0.5754
41 A A -0.4182
42 P A -0.2686
43 K A 0.3711
44 L A 1.5056
45 V A 0.0000
46 M A 0.0000
47 H A -1.5439
48 T A 0.0000
49 N A -1.5518
50 N A -2.2756
51 Q A -2.8118
52 R A -3.2289
53 P A -1.6113
54 S A -0.7465
55 G A 0.4444
56 V A 1.1052
57 P A 0.0660
58 D A -1.3315
59 R A -2.3507
60 F A 0.0000
61 S A -1.4180
62 G A 0.0000
63 S A -1.2693
64 R A -1.2281
65 S A -0.7846
66 G A -0.8313
67 T A -0.5868
68 S A -0.5637
69 A A 0.0000
70 S A -0.4542
71 L A 0.0000
72 A A -0.7581
73 I A 0.0000
74 S A -1.7653 mutated: GS74A
75 G A -1.2466
76 L A 0.0000
77 Q A 0.0000
78 S A -0.7636
79 E A -1.8514
80 D A -2.5283
81 E A -2.8727
82 A A 0.0000
83 D A -1.7078
84 Y A 0.0000
85 F A 0.5441
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.0000
90 D A -2.4019
91 D A -2.8209
92 N A -1.7548
93 L A -0.3384
94 N A -1.6189
95 G A -0.8606
96 V A 1.0515
97 I A 2.7572
98 F A 3.1834
99 G A 1.3919
100 G A 0.0131
101 G A -0.6926
102 T A 0.0000
103 K A -2.4203
104 L A 0.0000
105 T A -1.1536
106 V A 0.0000
107 L A 0.6225
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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, -0.5283 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_1 -0.5283 View CSV PDB
model_2 -0.5286 View CSV PDB
model_4 -0.6116 View CSV PDB
model_9 -0.6118 View CSV PDB
model_11 -0.6135 View CSV PDB
model_10 -0.6233 View CSV PDB
model_0 -0.6307 View CSV PDB
input -0.6555 View CSV PDB
model_5 -0.6595 View CSV PDB
model_7 -0.6632 View CSV PDB
model_8 -0.6844 View CSV PDB
model_6 -0.7145 View CSV PDB
model_3 -0.727 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018