Project name: DR5 10A

Status: done

submitted: 2019-04-02 03:10:06, status changed: 2019-04-02 05:31:20
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Chain sequence(s) C: EVQLLESGGGEVQPGGSLRLSCAASGLTFPNYGMGWFRQAPGKEREFVSAIYWSGGTVYYAESVKGRFTISRDNAKNTLYLQMSSLRAEDTAVYYCAVTIRGAATQTWKYDYWGQGTLVTVK
Distance of aggregation 10 Å
Dynamic mode Yes
Show buried residues
Minimal score value
-3.9399
Maximal score value
2.4264
Average score
-0.6262
Total score value
-76.3927

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 E C -1.1716
2 V C 0.5667
3 Q C 0.0188
4 L C 0.5412
5 L C 1.3034
6 E C 0.0000
7 S C -0.0903
8 G C -0.4623
9 G C -0.6618
10 G C 0.0000
11 E C -2.3761
12 V C 0.0000
13 Q C -2.7468
14 P C -1.9121
15 G C -1.3900
16 G C -0.9345
17 S C -1.2498
18 L C -1.3962
19 R C -1.9546
20 L C 0.0000
21 S C -0.2792
22 C C 0.0000
23 A C -0.0785
24 A C 0.0000
25 S C -0.4830
26 G C -0.6651
27 L C -0.3825
28 T C -0.5253
29 F C 0.0000
30 P C -0.7846
31 N C -1.0542
32 Y C 0.0000
33 G C -0.3240
34 M C 0.0000
35 G C 0.5581
36 W C 0.0000
37 F C 0.1923
38 R C 0.0000
39 Q C -2.0845
40 A C -2.1192
41 P C -1.7169
42 G C -2.1469
43 K C -3.5638
44 E C -3.9399
45 R C -3.6047
46 E C -2.0677
47 F C -0.6547
48 V C 0.0000
49 S C 0.0000
50 A C 1.2176
51 I C 0.0000
52 Y C 1.1642
53 W C 0.1439
54 S C -0.3204
55 G C -0.4243
56 G C 0.0318
57 T C 0.9453
58 V C 1.8396
59 Y C 2.4264
60 Y C 1.4722
61 A C 0.2851
62 E C -1.7259
63 S C 0.0000
64 V C 0.4196
65 K C -1.5724
66 G C -1.3816
67 R C -1.2866
68 F C 0.0000
69 T C -0.0579
70 I C 0.0000
71 S C -0.4120
72 R C -1.0159
73 D C -1.7614
74 N C -1.7117
75 A C -1.3572
76 K C -2.3051
77 N C -1.6283
78 T C -1.0243
79 L C 0.0000
80 Y C -0.5926
81 L C 0.0000
82 Q C -1.2085
83 M C 0.0000
84 S C -1.3372
85 S C -1.1556
86 L C 0.0000
87 R C -1.4231
88 A C -1.7927
89 E C -2.6750
90 D C 0.0000
91 T C -0.9165
92 A C 0.0000
93 V C 0.6416
94 Y C 0.0000
95 Y C 0.5189
96 C C 0.0000
97 A C 0.0000
98 V C 0.0000
99 T C -1.1183
100 I C 0.0000
101 R C -2.6817
102 G C 0.0000
103 A C -1.1631
104 A C -0.7812
105 T C -0.5608
106 Q C -1.6209
107 T C -1.0893
108 W C -0.9992
109 K C -2.2746
110 Y C -1.2415
111 D C -1.8403
112 Y C -0.3218
113 W C 0.3823
114 G C 0.2868
115 Q C -0.3350
116 G C -0.1594
117 T C 0.0000
118 L C 1.0999
119 V C 0.0000
120 T C -1.3078
121 V C 0.0000
122 K C -3.0465

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Above is the comparison between the input structure and the most aggregation prone model (predicted in the flexibility simulations, download both models in the PDB file format , download table with rmsd values ). The picture presents the most aggregation prone model (in blue) superimposed on the input structure (in red). The plot shows rmsd profile (distances between residues of the superimposed structures).

Dynamic mode uses CABS-flex simulations of protein structure fluctuations. The structure fluctuations may have impact on the size and extent of aggregation "hot-spots" on the protein surface. The dynamic mode uses the following pipeline: (1) based on the input structure, CABS-flex predicts a set of different models reflecting protein dynamics in solution; (2) for each of these models A3D score is calculated; (3) finally, the most aggregation prone model (the model with the highest A3D score, -0.6262 in this case) is selected and presented in A3D results.


 
Laboratory of Theory of Biopolymers 2015