Project name: f2c25c0651633a0 [mutate: RR64A]

Status: done

Started: 2020-04-05 14:02:58
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 RR64A
Energy difference between WT (input) and mutated protein (by FoldX) -0.702275 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                                                       (00:00:45)
[INFO]       FoldX:    Starting FoldX energy minimalization                                        (00:00:47)
[INFO]       CABS:     Running CABS flex simulation                                                (00:01:05)
[INFO]       Analysis: Starting Aggrescan3D on model_10.pdb                                        (00:22:50)
[INFO]       Analysis: Starting Aggrescan3D on model_7.pdb                                         (00:22:51)
[INFO]       Analysis: Starting Aggrescan3D on model_9.pdb                                         (00:22:53)
[INFO]       Analysis: Starting Aggrescan3D on model_8.pdb                                         (00:22:55)
[INFO]       Analysis: Starting Aggrescan3D on model_11.pdb                                        (00:22:55)
[INFO]       Analysis: Starting Aggrescan3D on model_6.pdb                                         (00:22:56)
[INFO]       Analysis: Starting Aggrescan3D on model_4.pdb                                         (00:22:56)
[INFO]       Analysis: Starting Aggrescan3D on model_2.pdb                                         (00:22:56)
[INFO]       Analysis: Starting Aggrescan3D on model_5.pdb                                         (00:22:57)
[INFO]       Analysis: Starting Aggrescan3D on model_1.pdb                                         (00:22:57)
[INFO]       Analysis: Starting Aggrescan3D on model_0.pdb                                         (00:22:57)
[INFO]       Analysis: Starting Aggrescan3D on model_3.pdb                                         (00:22:58)
[INFO]       Analysis: Starting Aggrescan3D on input.pdb                                           (00:22:58)
[INFO]       Analysis: Starting Aggrescan3D on folded.pdb                                          (00:23:01)
[INFO]       Movie:    Creting movie with webm format                                              (00:24:42)
[INFO]       Main:     Simulation completed successfully.                                          (00:24:45)
Show buried residues

Minimal score value
-3.2696
Maximal score value
2.5654
Average score
-0.5609
Total score value
-60.0129

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 0.8365
2 T A 0.3125
3 Q A 0.0000
4 P A -0.6059
5 P A -0.6371
6 S A -0.6626
7 T A 0.0000
8 S A -0.3292
9 G A 0.0000
10 T A -0.4329
11 P A -0.7741
12 G A -1.2591
13 Q A -1.6153
14 R A 0.0000
15 V A 0.2436
16 T A 0.0998
17 I A 0.0000
18 S A -0.5407
19 C A 0.0000
20 S A -0.4457
21 G A -0.0471
22 S A -0.3847
23 S A -0.1556
24 S A -0.1474
25 N A 0.1171
26 I A 1.1561
27 E A -0.1582
28 T A -0.5880
29 N A -1.0451
30 T A -0.5422
31 V A 0.0000
32 N A 0.0000
33 W A 0.0000
34 Y A 0.4677
35 Q A 0.0000
36 Q A -1.5236
37 L A 0.0000
38 P A -1.5839
39 G A -1.0922
40 T A -0.7893
41 A A -0.6127
42 P A -0.9164
43 K A -1.0022
44 L A 0.4761
45 V A 0.0000
46 M A 0.0000
47 H A -1.3948
48 T A -2.0067
49 N A -2.2789
50 N A -2.6706
51 Q A -3.0308
52 R A -2.8616
53 P A -1.7997
54 S A -1.0167
55 G A -0.8434
56 V A 0.8086
57 P A -0.6512
58 D A -2.0026
59 R A -1.6276
60 F A 0.0000
61 S A -1.4674
62 G A -1.0859
63 S A -1.3711
64 R A -2.3032 mutated: RR64A
65 S A -1.4959
66 G A -1.1240
67 T A -1.0586
68 S A -1.0681
69 A A 0.0000
70 S A -0.8922
71 L A 0.0000
72 A A -0.2118
73 I A 0.0000
74 G A -1.3430
75 G A -1.5252
76 L A 0.0000
77 Q A -1.5636
78 S A -1.3326
79 E A -2.3052
80 D A -2.9961
81 E A -3.2696
82 A A 0.0000
83 D A -1.8371
84 Y A 0.0000
85 F A 0.3716
86 C A 0.0000
87 A A 0.0000
88 A A 0.0000
89 W A 0.9358
90 D A 0.0174
91 D A -0.4544
92 N A -0.8469
93 L A 0.4119
94 N A -0.5123
95 G A 0.2624
96 V A 1.7981
97 I A 2.3636
98 F A 2.5654
99 G A 0.6407
100 G A -0.0878
101 G A -0.6903
102 T A 0.0000
103 K A -2.1018
104 L A 0.0000
105 T A -1.3589
106 V A 0.0000
107 L A 0.4810
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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, -0.5609 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_2 -0.5609 View CSV PDB
model_1 -0.6118 View CSV PDB
model_3 -0.6602 View CSV PDB
input -0.6628 View CSV PDB
model_7 -0.666 View CSV PDB
model_8 -0.6785 View CSV PDB
model_10 -0.7056 View CSV PDB
model_6 -0.7257 View CSV PDB
model_9 -0.759 View CSV PDB
model_11 -0.7666 View CSV PDB
model_5 -0.7679 View CSV PDB
model_0 -0.775 View CSV PDB
model_4 -0.8213 View CSV PDB
 

Laboratory of Theory of Biopolymers 2018