Aggrescan3D: bind7

Project name: bind7

Status: done

submitted: 2018-10-31 19:24:01, status changed: 2018-11-24 16:04:13

Settings

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

Drag cursor over the plot to display residue labels.

Show buried residues

Minimal score value: -3.9383
Maximal score value: 1.6268
Average score: -1.0574
Total score value: -138.5203

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	V	A	-0.7982
2	E	A	-1.9457
3	A	A	-0.8063
4	F	A	0.0000
5	C	A	0.6556
6	A	A	0.4803
7	T	A	0.1406
8	W	A	0.0000
9	K	A	-1.6870
10	L	A	-1.3344
11	T	A	-1.3435
12	N	A	-1.9534
13	S	A	-1.7455
14	Q	A	-2.1287
15	N	A	-2.1538
16	F	A	0.0000
17	D	A	-2.9414
18	E	A	-3.1486
19	Y	A	0.0000
20	M	A	-1.3117
21	K	A	-2.0986
22	A	A	-1.2135
23	L	A	-0.5634
24	G	A	-0.2359
25	V	A	0.9393
26	G	A	0.5527
27	F	A	0.5308
28	A	A	0.7589
29	T	A	0.6150
30	R	A	-0.6090
31	Q	A	0.2076
32	V	A	1.1139
33	G	A	-0.3901
34	N	A	-1.2299
35	V	A	-0.2701
36	T	A	-1.0690
37	K	A	-2.0188
38	P	A	0.0000
39	T	A	-0.3021
40	V	A	0.6318
41	I	A	1.6268
42	I	A	0.0000
43	S	A	0.1057
44	Q	A	-1.6002
45	E	A	-3.0716
46	G	A	-2.8485
47	D	A	-3.0453
48	K	A	-2.3742
49	V	A	0.0000
50	V	A	-0.0454
51	I	A	0.4583
52	R	A	-0.7856
53	T	A	-0.5617
54	L	A	-0.1785
55	S	A	-0.0952
56	T	A	0.1468
57	F	A	1.0271
58	K	A	-1.1119
59	N	A	-1.3337
60	T	A	-1.5174
61	E	A	-1.2875
62	I	A	0.2693
63	S	A	0.0296
64	F	A	-0.5370
65	Q	A	-1.9787
66	L	A	-1.9201
67	G	A	-2.0530
68	E	A	-2.1791
69	E	A	-2.6952
70	F	A	-1.7947
71	D	A	-2.8835
72	E	A	-2.1368
73	T	A	-2.3115
74	T	A	-1.9321
75	A	A	-2.0926
76	D	A	-3.1542
77	D	A	-3.6642
78	R	A	-3.7530
79	N	A	-3.9383
80	C	A	0.0000
81	K	A	-3.1795
82	S	A	0.0000
83	V	A	0.2252
84	V	A	0.0000
85	S	A	-0.3582
86	L	A	-0.8575
87	D	A	-2.2261
88	G	A	-2.0440
89	D	A	-2.8184
90	K	A	-1.9718
91	L	A	-0.4121
92	V	A	0.2874
93	H	A	0.4892
94	I	A	0.7930
95	Q	A	0.0000
96	K	A	-3.5973
97	W	A	-3.3632
98	D	A	-3.8022
99	G	A	-3.1474
100	K	A	-3.6895
101	E	A	-3.7283
102	T	A	0.0000
103	N	A	-1.0445
104	F	A	0.3328
105	V	A	0.4970
106	R	A	0.0000
107	E	A	-1.6362
108	I	A	-2.1749
109	K	A	-3.3283
110	D	A	-3.3780
111	G	A	-2.4375
112	K	A	-2.5166
113	M	A	0.0000
114	V	A	-0.1682
115	M	A	0.3803
116	T	A	0.6650
117	L	A	0.0000
118	T	A	0.2112
119	F	A	-0.4207
120	G	A	-1.2143
121	D	A	-1.4989
122	V	A	-0.6506
123	V	A	0.6073
124	A	A	0.0000
125	V	A	0.1844
126	R	A	0.0000
127	H	A	-0.8908
128	Y	A	0.0000
129	E	A	-2.1105
130	K	A	-1.7361
131	A	A	-0.9023

Download PDB file

View in JSmol

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, -1.0574 in this case) is selected and presented in A3D results.