Aggrescan3D: 1pht_dyn

Project name: 1pht_dyn_Valen

Status: done

submitted: 2019-01-25 15:24:31, status changed: 2019-01-25 17:36:33

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

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Minimal score value: -4.6223
Maximal score value: 1.7546
Average score: -0.9536
Total score value: -79.1467

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	A	A	-0.4890
4	E	A	-1.7272
5	G	A	0.0000
6	Y	A	0.0000
7	Q	A	-0.4096
8	Y	A	0.0000
9	R	A	-0.1313
10	A	A	0.0000
11	L	A	0.9505
12	Y	A	0.0000
13	D	A	-2.1866
14	Y	A	-1.9604
15	K	A	-3.5479
16	K	A	-3.5499
17	E	A	-4.1800
18	R	A	-4.6223
19	E	A	-4.3660
20	E	A	-3.7721
21	D	A	0.0000
22	I	A	0.0000
23	D	A	-3.7078
24	L	A	0.0000
25	H	A	-2.1440
26	L	A	-0.5793
27	G	A	-0.4230
28	D	A	-0.1106
29	I	A	1.2062
30	L	A	0.0000
31	T	A	0.0000
32	V	A	0.0000
33	N	A	-0.7591
34	K	A	-0.5343
35	G	A	-0.1762
36	S	A	0.2432
37	L	A	0.0000
38	V	A	1.7546
39	A	A	1.2017
40	L	A	1.7446
41	G	A	0.7171
42	F	A	0.0000
43	S	A	-1.2899
44	D	A	-2.6508
45	G	A	-2.3184
46	Q	A	-3.0236
47	E	A	0.0000
48	A	A	-2.3927
49	R	A	-3.6771
50	P	A	0.0000
51	E	A	-3.1915
52	E	A	-3.2339
53	I	A	-1.8750
54	G	A	-0.6922
55	W	A	0.3060
56	L	A	0.0000
57	N	A	-0.4284
58	G	A	0.0000
59	Y	A	-0.5614
60	N	A	0.0000
61	E	A	-1.9435
62	T	A	-0.9259
63	T	A	-1.3400
64	G	A	-1.6418
65	E	A	-2.0110
66	R	A	-2.3951
67	G	A	0.0000
68	D	A	-1.2423
69	F	A	0.0000
70	P	A	-0.2410
71	G	A	-0.9400
72	T	A	-0.6889
73	Y	A	0.3166
74	V	A	0.0000
75	E	A	-1.5781
76	Y	A	-1.1044
77	I	A	0.1631
78	G	A	-0.9356
79	R	A	-2.5802
80	K	A	-2.0959
81	K	A	-1.7651
82	I	A	0.6613
83	S	A	-0.0006
84	P	A	-0.0980
85	P	A	-0.1727

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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, -0.9536 in this case) is selected and presented in A3D results.