Aggrescan3D: bind5

Project name: bind5

Status: done

submitted: 2018-10-31 19:23:34, status changed: 2018-11-24 16:04:13

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

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Minimal score value: -3.2281
Maximal score value: 1.3398
Average score: -0.9639
Total score value: -128.2008

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
3	T	A	-0.9441
4	V	A	-1.3144
5	Q	A	-2.4695
6	Q	A	-2.3759
7	L	A	0.0000
8	E	A	-2.4034
9	G	A	0.0000
10	R	A	-1.1838
11	W	A	0.0000
12	R	A	-1.7661
13	L	A	-0.2610
14	V	A	0.8960
15	D	A	-0.3519
16	S	A	-0.6852
17	K	A	-2.0332
18	G	A	0.0000
19	F	A	-1.5457
20	D	A	-2.2905
21	E	A	-3.1491
22	Y	A	-2.1030
23	M	A	0.0000
24	K	A	-2.9586
25	E	A	-3.2227
26	L	A	0.0000
27	G	A	-1.3899
28	V	A	-0.0597
29	G	A	0.3626
30	I	A	1.3398
31	A	A	0.7208
32	L	A	0.8165
33	R	A	-0.5268
34	K	A	-0.8817
35	M	A	0.2489
36	G	A	-0.0351
37	A	A	-0.1748
38	M	A	0.5319
39	A	A	-0.0895
40	K	A	-0.8501
41	P	A	-0.7101
42	D	A	0.0000
43	C	A	0.0000
44	I	A	-0.0920
45	I	A	0.0000
46	T	A	-1.3223
47	C	A	0.0000
48	D	A	-2.5811
49	G	A	-2.4027
50	K	A	-2.9506
51	N	A	-2.2934
52	L	A	0.0000
53	T	A	-0.7405
54	I	A	-0.1241
55	K	A	-0.6262
56	T	A	-0.7005
57	E	A	-0.7148
58	S	A	-0.3589
59	T	A	0.0569
60	L	A	1.1286
61	K	A	-0.1540
62	T	A	-0.5911
63	T	A	-0.7071
64	Q	A	-1.0633
65	F	A	-0.3554
66	S	A	-0.4356
67	C	A	0.0000
68	T	A	-1.4906
69	L	A	-1.8138
70	G	A	-2.1092
71	E	A	-2.7391
72	K	A	-2.1539
73	F	A	-0.9140
74	E	A	-1.6358
75	E	A	0.0000
76	T	A	-1.7115
77	T	A	-1.4605
78	A	A	-1.6267
79	D	A	-2.5360
80	G	A	-2.2751
81	R	A	-2.9636
82	K	A	-3.2281
83	T	A	0.0000
84	Q	A	-1.9711
85	T	A	0.0000
86	V	A	-1.0307
87	C	A	0.0000
88	N	A	-1.4912
89	F	A	-0.8176
90	T	A	-1.0006
91	D	A	-1.8726
92	G	A	-1.2929
93	A	A	-1.0693
94	L	A	0.0000
95	V	A	-0.0198
96	Q	A	0.0000
97	H	A	-0.2989
98	Q	A	-1.0594
99	E	A	-2.2891
100	W	A	-2.3115
101	D	A	-3.0620
102	G	A	-2.2993
103	K	A	-2.7204
104	E	A	-2.1557
105	S	A	0.0000
106	T	A	0.0390
107	I	A	0.3515
108	T	A	-0.0370
109	R	A	0.0000
110	K	A	-1.6547
111	L	A	-1.7334
112	K	A	-3.0797
113	D	A	-3.1376
114	G	A	-2.6145
115	K	A	-3.1624
116	L	A	0.0000
117	V	A	-0.3149
118	V	A	0.0000
119	E	A	-0.2212
120	C	A	0.6340
121	V	A	0.5648
122	M	A	0.0000
123	N	A	-2.0833
124	N	A	-1.9357
125	V	A	-0.9774
126	T	A	-0.3948
127	C	A	0.0000
128	T	A	-0.1853
129	R	A	0.0587
130	I	A	0.4917
131	Y	A	0.0000
132	E	A	-1.6043
133	K	A	-1.6864
134	V	A	-0.4722
135	E	A	-1.7383

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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, -0.9639 in this case) is selected and presented in A3D results.