Aggrescan3D: newA3D

Project name: newA3D

Status: done

submitted: 2019-01-30 15:13:34, status changed: 2019-01-30 17:35:21

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Chain sequence(s)	A: CDLPQTHSLGSRRTLMLLAQMRKISLFSCLKDRHDFGFPQEEFGNQFQKAETIPVLHEMIQQIFNLFSTKDSSAAWDETLLDKFYTELYQQLNDLEACVIQGVGVTETPLMKEDSILAVRKYFQRITLYLKEKKYSPCAWEVVRAEIMRSFSLSTNLQESLRSKE
Distance of aggregation	10 Å
Dynamic mode	Yes

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Minimal score value: -3.6725
Maximal score value: 2.6691
Average score: -0.6005
Total score value: -99.0758

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	C	A	-0.3373
2	D	A	-1.8971
3	L	A	-1.0602
4	P	A	-0.8133
5	Q	A	-0.9773
6	T	A	-0.4766
7	H	A	0.0000
8	S	A	-0.0302
9	L	A	0.8097
10	G	A	-0.1025
11	S	A	0.0000
12	R	A	-0.0130
13	R	A	-0.3105
14	T	A	0.0000
15	L	A	0.3357
16	M	A	0.7131
17	L	A	0.0169
18	L	A	0.0000
19	A	A	-0.3115
20	Q	A	-0.8673
21	M	A	0.0000
22	R	A	-0.9162
23	K	A	-1.6070
24	I	A	0.0613
25	S	A	0.8906
26	L	A	2.1191
27	F	A	2.4702
28	S	A	0.8890
29	C	A	0.0000
30	L	A	0.8518
31	K	A	-1.1610
32	D	A	-1.8922
33	R	A	-2.0362
34	H	A	-2.0206
35	D	A	-2.4178
36	F	A	-1.1932
37	G	A	-1.0887
38	F	A	0.0000
39	P	A	-1.3677
40	Q	A	-2.0739
41	E	A	-3.0240
42	E	A	-2.4113
43	F	A	0.0000
44	G	A	-1.5315
45	N	A	-1.8196
46	Q	A	-0.5904
47	F	A	0.3793
48	Q	A	-0.7099
49	K	A	-0.6911
50	A	A	0.4569
51	E	A	0.0000
52	T	A	0.0000
53	I	A	0.0000
54	P	A	-0.2594
55	V	A	0.0000
56	L	A	0.0000
57	H	A	-0.4598
58	E	A	-0.4491
59	M	A	0.0000
60	I	A	0.0000
61	Q	A	-0.5490
62	Q	A	-0.9481
63	I	A	0.0000
64	F	A	0.4394
65	N	A	-0.9242
66	L	A	-0.7091
67	F	A	0.0000
68	S	A	-0.8873
69	T	A	-1.5249
70	K	A	-2.6316
71	D	A	-2.2357
72	S	A	0.0000
73	S	A	-2.0442
74	A	A	-1.9332
75	A	A	-1.3843
76	W	A	0.0000
77	D	A	-2.7450
78	E	A	-3.2047
79	T	A	-2.0038
80	L	A	-1.3026
81	L	A	-1.4327
82	D	A	-2.0162
83	K	A	-1.1550
84	F	A	0.0000
85	Y	A	0.5230
86	T	A	0.2162
87	E	A	0.0000
88	L	A	0.0000
89	Y	A	0.9335
90	Q	A	-0.4617
91	Q	A	0.0000
92	L	A	-0.3488
93	N	A	-1.5119
94	D	A	-1.0948
95	L	A	0.0000
96	E	A	-0.7372
97	A	A	-0.2005
98	C	A	0.0000
99	V	A	1.3242
100	I	A	2.2171
101	Q	A	0.0781
102	G	A	0.6815
103	V	A	2.6691
104	G	A	1.5059
105	V	A	2.1601
106	T	A	0.0984
107	E	A	-1.2311
108	T	A	-0.4275
109	P	A	-0.6137
110	L	A	0.5389
111	M	A	-0.3059
112	K	A	-0.8844
113	E	A	-1.2596
114	D	A	-1.9405
115	S	A	0.0000
116	I	A	-0.7695
117	L	A	-0.4296
118	A	A	-1.2736
119	V	A	0.0000
120	R	A	-1.9744
121	K	A	-2.4387
122	Y	A	-1.0377
123	F	A	0.0000
124	Q	A	-1.9225
125	R	A	-1.1817
126	I	A	0.0000
127	T	A	-0.9827
128	L	A	-0.4810
129	Y	A	-1.4688
130	L	A	0.0000
131	K	A	-3.2299
132	E	A	-3.4910
133	K	A	-3.6725
134	K	A	-3.4702
135	Y	A	-1.8869
136	S	A	-0.9684
137	P	A	-0.3113
138	C	A	0.2266
139	A	A	0.0000
140	W	A	0.0000
141	E	A	0.0000
142	V	A	0.0000
143	V	A	0.0000
144	R	A	0.0000
145	A	A	0.0000
146	E	A	0.0000
147	I	A	0.0000
148	M	A	-0.0074
149	R	A	-0.6147
150	S	A	0.0000
151	F	A	0.0000
152	S	A	-0.5016
153	L	A	-0.6976
154	S	A	0.0000
155	T	A	0.0000
156	N	A	-1.0557
157	L	A	0.0000
158	Q	A	0.0000
159	E	A	-1.0124
160	S	A	-0.6972
161	L	A	-0.2223
162	R	A	-1.7072
163	S	A	-1.8501
164	K	A	-2.8489
165	E	A	-2.9093

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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, -0.6005 in this case) is selected and presented in A3D results.