Aggrescan3D: nano

Project name: nano

Status: done

submitted: 2018-11-19 06:11:35, status changed: 2018-11-24 16:29:12

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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: -2.0254
Maximal score value: 1.6213
Average score: -0.2504
Total score value: -30.5444

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	-1.4886
2	V	C	1.2029
3	Q	C	-0.8230
4	L	C	0.2473
5	L	C	1.5306
6	E	C	0.0043
7	S	C	-0.2837
8	G	C	-0.2394
9	G	C	-0.4869
10	G	C	0.0000
11	E	C	-1.8214
12	V	C	0.0000
13	Q	C	-1.2443
14	P	C	-0.5034
15	G	C	-0.3141
16	G	C	-0.5371
17	S	C	-0.2558
18	L	C	-0.1924
19	R	C	-1.8664
20	L	C	0.0000
21	S	C	-0.0269
22	C	C	0.0000
23	A	C	0.0181
24	A	C	0.0000
25	S	C	-0.2129
26	G	C	-0.3219
27	L	C	0.0000
28	T	C	-0.0346
29	F	C	0.1714
30	P	C	-0.2337
31	N	C	-0.9534
32	Y	C	0.0000
33	G	C	0.0046
34	M	C	0.0000
35	G	C	0.0000
36	W	C	0.0000
37	F	C	0.3530
38	R	C	0.0000
39	Q	C	-0.5871
40	A	C	0.0000
41	P	C	-0.3416
42	G	C	-0.8157
43	K	C	-1.9928
44	E	C	-1.6247
45	R	C	-1.2413
46	E	C	0.0000
47	F	C	0.3901
48	V	C	0.0000
49	S	C	0.0000
50	A	C	0.0057
51	I	C	0.0000
52	Y	C	1.1318
53	W	C	0.3244
54	S	C	-0.2477
55	G	C	-0.5389
56	G	C	-0.4015
57	T	C	0.0150
58	V	C	0.9068
59	Y	C	1.5540
60	Y	C	0.8911
61	A	C	-0.1855
62	E	C	-1.8184
63	S	C	0.0000
64	V	C	1.4725
65	K	C	-1.4028
66	G	C	-0.7519
67	R	C	-1.8605
68	F	C	0.0000
69	T	C	-0.0709
70	I	C	0.0000
71	S	C	-0.1530
72	R	C	-0.7069
73	D	C	-0.8716
74	N	C	-1.1727
75	A	C	-0.4158
76	K	C	-1.8703
77	N	C	-0.7437
78	T	C	-0.1580
79	L	C	0.0000
80	Y	C	0.3456
81	L	C	0.0000
82	Q	C	-0.6842
83	M	C	0.0000
84	S	C	-0.0857
85	S	C	-0.1777
86	L	C	0.0000
87	R	C	-0.9510
88	A	C	-0.4523
89	E	C	-1.8090
90	D	C	0.0000
91	T	C	-0.0186
92	A	C	0.0000
93	V	C	0.8528
94	Y	C	0.0000
95	Y	C	0.2977
96	C	C	0.0000
97	A	C	0.0000
98	V	C	0.0000
99	T	C	-0.1836
100	I	C	0.0000
101	R	C	-2.0254
102	G	C	0.0000
103	A	C	0.0692
104	A	C	0.0564
105	T	C	-0.1776
106	Q	C	-0.7209
107	T	C	-0.1291
108	W	C	0.0093
109	K	C	-1.5897
110	Y	C	0.8055
111	D	C	-0.8127
112	Y	C	0.0775
113	W	C	0.6563
114	G	C	0.0000
115	Q	C	-1.2464
116	G	C	-0.6922
117	T	C	0.0000
118	L	C	1.6213
119	V	C	0.0000
120	T	C	-0.1717
121	V	C	-0.1521
122	K	C	-1.6665

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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, -0.2504 in this case) is selected and presented in A3D results.