Aggrescan3D: Ras-GDP test

Project name: Ras-GDP test

Status: done

submitted: 2018-12-11 07:03:11, status changed: 2018-12-11 09:26:01

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Chain sequence(s)	A: MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHQYREQIKRVKDSDDVPMVLVGNKCDLAARTVESRQAQDLARSYGIPYIETSAKTRQGVEDAFYTLVREIRQHKLRKL
Distance of aggregation	5 Å
Dynamic mode	Yes

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Minimal score value: -2.1941
Maximal score value: 2.1352
Average score: -0.4165
Total score value: -71.2268

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	M	A	1.0505
2	T	A	-0.1177
3	E	A	-1.6197
4	Y	A	0.0000
5	K	A	-0.6732
6	L	A	0.0000
7	V	A	0.0000
8	V	A	0.0000
9	V	A	0.0000
10	G	A	0.0000
11	A	A	-0.0735
12	G	A	-0.2883
13	G	A	-0.5038
14	V	A	0.0000
15	G	A	-0.1429
16	K	A	0.0000
17	S	A	0.0000
18	A	A	0.0056
19	L	A	0.0000
20	T	A	0.0000
21	I	A	0.0000
22	Q	A	0.0000
23	L	A	0.0000
24	I	A	0.2141
25	Q	A	-0.9332
26	N	A	-1.5973
27	H	A	-0.9578
28	F	A	1.6291
29	V	A	1.8730
30	D	A	-0.8385
31	E	A	-1.7351
32	Y	A	0.6440
33	D	A	-1.5829
34	P	A	-0.5443
35	T	A	-0.1231
36	I	A	-0.1426
37	E	A	-1.9599
38	D	A	-1.3346
39	S	A	-0.2796
40	Y	A	-0.1774
41	R	A	-1.8513
42	K	A	-0.7613
43	Q	A	-1.1974
44	V	A	0.0000
45	V	A	2.1352
46	I	A	2.0180
47	D	A	-1.5714
48	G	A	-0.8619
49	E	A	-0.6473
50	T	A	0.1509
51	C	A	0.0000
52	L	A	0.0121
53	L	A	0.0000
54	D	A	-0.7479
55	I	A	0.0000
56	L	A	0.1849
57	D	A	0.0000
58	T	A	0.0000
59	A	A	0.0000
60	G	A	-0.4996
61	Q	A	-0.3754
62	E	A	-2.1941
63	E	A	-1.9272
64	Y	A	0.9226
65	S	A	0.0320
66	A	A	-0.0312
67	M	A	0.0000
68	R	A	-2.0077
69	D	A	-1.4316
70	Q	A	-1.3009
71	Y	A	-0.1267
72	M	A	0.0000
73	R	A	-1.8242
74	T	A	-0.4087
75	G	A	0.0000
76	E	A	-0.9293
77	G	A	0.0000
78	F	A	0.0000
79	L	A	0.0000
80	C	A	0.0000
81	V	A	0.0000
82	F	A	0.0000
83	A	A	0.0372
84	I	A	0.2917
85	N	A	-0.5045
86	N	A	-1.3427
87	T	A	-0.5915
88	K	A	-1.9286
89	S	A	-0.3391
90	F	A	0.0000
91	E	A	-2.0829
92	D	A	-0.7516
93	I	A	0.0000
94	H	A	-0.3200
95	Q	A	-0.7977
96	Y	A	0.0042
97	R	A	0.0000
98	E	A	-0.8727
99	Q	A	-0.3762
100	I	A	0.0000
101	K	A	-0.9589
102	R	A	-2.1271
103	V	A	0.1915
104	K	A	-0.6049
105	D	A	-2.1676
106	S	A	-0.8001
107	D	A	-2.0840
108	D	A	-1.8241
109	V	A	0.0000
110	P	A	-0.0276
111	M	A	0.0000
112	V	A	0.0000
113	L	A	0.0000
114	V	A	0.0000
115	G	A	0.0000
116	N	A	0.0000
117	K	A	-0.1104
118	C	A	0.1534
119	D	A	-1.3774
120	L	A	1.1986
121	A	A	0.3286
122	A	A	-0.2807
123	R	A	-1.8461
124	T	A	-0.4750
125	V	A	0.0000
126	E	A	-0.6627
127	S	A	-0.6372
128	R	A	-1.9882
129	Q	A	-1.0737
130	A	A	0.0000
131	Q	A	-0.7533
132	D	A	-0.9895
133	L	A	0.1113
134	A	A	0.0000
135	R	A	-1.9559
136	S	A	-0.5504
137	Y	A	0.0000
138	G	A	-0.3324
139	I	A	0.0000
140	P	A	-0.1101
141	Y	A	0.2441
142	I	A	0.0000
143	E	A	-1.8199
144	T	A	0.0000
145	S	A	-0.0573
146	A	A	0.0000
147	K	A	-1.7136
148	T	A	-0.7094
149	R	A	-1.9757
150	Q	A	-1.5317
151	G	A	0.0000
152	V	A	0.0000
153	E	A	-1.1896
154	D	A	-1.9480
155	A	A	0.0000
156	F	A	0.0000
157	Y	A	1.0218
158	T	A	0.1003
159	L	A	0.0000
160	V	A	0.0000
161	R	A	-0.8867
162	E	A	-0.4249
163	I	A	0.0000
164	R	A	-0.7400
165	Q	A	-0.7793
166	H	A	-0.5784
167	K	A	-0.4661
168	L	A	1.2451
169	R	A	-1.8862
170	K	A	-1.7555
171	L	A	1.4010

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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, -0.4165 in this case) is selected and presented in A3D results.