Aggrescan3D: nano

Project name: nano_rerun

Status: done

submitted: 2018-11-24 16:06:34, status changed: 2018-11-24 18:24:11

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Chain sequence(s)	C: EVQLLESGGGEVQPGGSLRLSCAASGLTFPNYGMGWFRQAPGKEREFVSAIYWSGGTVYYAESVKGRFTISRDNAKNTLYLQMSSLRAEDTAVYYCAVTIRGAATQTWKYDYWGQGTLVTVK
Distance of aggregation	5 Å
Dynamic mode	Yes

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Show buried residues

Minimal score value: -2.504
Maximal score value: 1.6194
Average score: -0.2541
Total score value: -30.9972

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	-1.4761
2	V	C	1.2797
3	Q	C	-0.3989
4	L	C	0.3290
5	L	C	1.4693
6	E	C	0.0000
7	S	C	-0.1988
8	G	C	-0.2527
9	G	C	-0.4908
10	G	C	0.0000
11	E	C	-1.8199
12	V	C	0.0000
13	Q	C	-1.2382
14	P	C	-0.4930
15	G	C	-0.2593
16	G	C	-0.5226
17	S	C	-0.2298
18	L	C	-0.1799
19	R	C	-1.8430
20	L	C	0.0000
21	S	C	-0.0256
22	C	C	0.0000
23	A	C	0.0137
24	A	C	0.0000
25	S	C	-0.2998
26	G	C	-0.4760
27	L	C	0.0669
28	T	C	-0.0378
29	F	C	0.0000
30	P	C	-0.1668
31	N	C	-0.5820
32	Y	C	0.0000
33	G	C	-0.0827
34	M	C	0.0000
35	G	C	-0.0474
36	W	C	0.0000
37	F	C	0.6074
38	R	C	0.0000
39	Q	C	-0.8475
40	A	C	-0.1427
41	P	C	-0.3376
42	G	C	-0.8353
43	K	C	-2.1499
44	E	C	-2.5040
45	R	C	-2.3129
46	E	C	-0.5598
47	F	C	0.2508
48	V	C	0.0000
49	S	C	0.0000
50	A	C	0.0071
51	I	C	0.0000
52	Y	C	1.1457
53	W	C	0.4448
54	S	C	-0.3038
55	G	C	-0.5306
56	G	C	-0.1921
57	T	C	0.1933
58	V	C	1.1969
59	Y	C	1.6167
60	Y	C	0.8976
61	A	C	-0.1718
62	E	C	-1.8182
63	S	C	0.0000
64	V	C	1.4853
65	K	C	-1.4096
66	G	C	-0.5958
67	R	C	-1.2309
68	F	C	0.0000
69	T	C	-0.0588
70	I	C	0.0000
71	S	C	-0.1825
72	R	C	-0.8641
73	D	C	-0.8476
74	N	C	-0.7731
75	A	C	-0.3411
76	K	C	-1.8054
77	N	C	-0.6355
78	T	C	-0.1311
79	L	C	0.0000
80	Y	C	0.3634
81	L	C	0.0000
82	Q	C	-0.4962
83	M	C	0.0000
84	S	C	-0.0728
85	S	C	-0.1486
86	L	C	0.0000
87	R	C	-0.6969
88	A	C	-0.3821
89	E	C	-1.8097
90	D	C	0.0000
91	T	C	-0.0263
92	A	C	0.0000
93	V	C	0.8512
94	Y	C	0.0000
95	Y	C	0.2934
96	C	C	0.0000
97	A	C	0.0000
98	V	C	0.0000
99	T	C	-0.2947
100	I	C	0.0000
101	R	C	-1.8441
102	G	C	0.0000
103	A	C	0.0659
104	A	C	0.0557
105	T	C	-0.2612
106	Q	C	-1.2228
107	T	C	-0.2287
108	W	C	-0.0291
109	K	C	-1.4391
110	Y	C	0.4813
111	D	C	-1.5402
112	Y	C	0.0561
113	W	C	1.1614
114	G	C	-0.0717
115	Q	C	-1.2541
116	G	C	-0.7065
117	T	C	0.0000
118	L	C	1.6194
119	V	C	0.0000
120	T	C	-0.0216
121	V	C	0.0000
122	K	C	-1.7000

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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, -0.2541 in this case) is selected and presented in A3D results.