Aggrescan3D: apoFab

Project name: apoFab

Status: done

submitted: 2019-03-09 02:26:53, status changed: 2019-03-09 04:49:38

Settings

Chain sequence(s)	L: DIQMTQSPSSLSASVGDRVTITCRASQSISSYLNWYQQKPGKAPKLLIYAASSLQSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSYSTPLTFGGGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNR
Distance of aggregation	10 Å
Dynamic mode	Yes

Drag cursor over the plot to display residue labels.

Show buried residues

Minimal score value: -3.564
Maximal score value: 2.4511
Average score: -0.5933
Total score value: -125.1961

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	D	L	-2.0379
2	I	L	-1.1201
3	Q	L	-1.5125
4	M	L	0.0000
5	T	L	-0.6393
6	Q	L	0.0000
7	S	L	-0.5299
8	P	L	-0.4256
9	S	L	-0.6099
10	S	L	-0.5930
11	L	L	-0.2256
12	S	L	-0.5251
13	A	L	-1.0044
14	S	L	-0.6781
15	V	L	-0.3151
16	G	L	-1.5498
17	D	L	-2.5796
18	R	L	-2.8378
19	V	L	0.0000
20	T	L	-0.8481
21	I	L	0.0000
22	T	L	-0.3985
23	C	L	0.0000
24	R	L	-1.7481
25	A	L	0.0000
26	S	L	-1.7185
27	Q	L	-2.0606
28	S	L	-1.0719
29	I	L	0.0000
30	S	L	-0.3749
31	S	L	0.1618
32	Y	L	0.7122
33	L	L	0.0000
34	N	L	0.0000
35	W	L	0.0000
36	Y	L	0.5258
37	Q	L	0.0000
38	Q	L	-0.6513
39	K	L	0.0000
40	P	L	-0.4186
41	G	L	-1.2133
42	K	L	-2.1720
43	A	L	-1.3642
44	P	L	-0.9371
45	K	L	-1.0089
46	L	L	0.3544
47	L	L	0.0000
48	I	L	1.0908
49	Y	L	0.0000
50	A	L	0.3483
51	A	L	0.2037
52	S	L	-0.0476
53	S	L	0.0833
54	L	L	-0.2578
55	Q	L	-0.9335
56	S	L	-0.7824
57	G	L	-0.9821
58	V	L	-0.5851
59	P	L	-0.7344
60	S	L	-1.2500
61	R	L	-1.9632
62	F	L	0.0000
63	S	L	-0.5950
64	G	L	-0.3708
65	S	L	-0.5953
66	G	L	-0.8689
67	S	L	-0.7297
68	G	L	-0.8940
69	T	L	-1.1010
70	D	L	-1.2696
71	F	L	-0.6066
72	T	L	-0.5297
73	L	L	0.0000
74	T	L	-0.8293
75	I	L	0.0000
76	S	L	-1.9055
77	S	L	-1.6849
78	L	L	0.0000
79	Q	L	-1.0048
80	P	L	-1.2318
81	E	L	-1.6673
82	D	L	-0.6190
83	F	L	0.8873
84	A	L	0.0000
85	T	L	-0.0496
86	Y	L	0.0000
87	Y	L	0.7487
88	C	L	0.0000
89	Q	L	0.0000
90	Q	L	0.0000
91	S	L	1.1338
92	Y	L	0.8229
93	S	L	0.2708
94	T	L	0.3008
95	P	L	0.4244
96	L	L	1.6158
97	T	L	1.1709
98	F	L	2.0028
99	G	L	0.4505
100	G	L	-0.2011
101	G	L	-0.3221
102	T	L	0.0000
103	K	L	-0.5579
104	V	L	0.0000
105	E	L	-0.3237
106	I	L	0.0000
107	K	L	-1.4872
108	R	L	-1.7149
109	T	L	-0.2988
110	V	L	0.8030
111	A	L	0.7515
112	A	L	0.6127
113	P	L	0.6038
114	S	L	0.6315
115	V	L	1.4608
116	F	L	2.4511
117	I	L	2.2881
118	F	L	2.3746
119	P	L	0.6834
120	P	L	-0.7621
121	S	L	-1.7337
122	D	L	-3.3620
123	E	L	-3.5106
124	Q	L	-2.4825
125	L	L	-2.2059
126	K	L	-3.1330
127	S	L	-1.8714
128	G	L	-1.6483
129	T	L	-0.7528
130	A	L	0.0000
131	S	L	0.0689
132	V	L	0.0000
133	V	L	1.2470
134	C	L	0.0000
135	L	L	1.8378
136	L	L	0.0000
137	N	L	0.6282
138	N	L	0.0000
139	F	L	1.0167
140	Y	L	0.6893
141	P	L	0.0000
142	R	L	-1.2476
143	E	L	-1.7407
144	A	L	-1.4830
145	K	L	-1.9629
146	V	L	-1.2803
147	Q	L	-0.9617
148	W	L	0.0000
149	K	L	-0.8165
150	V	L	-1.2563
151	D	L	-2.0612
152	N	L	-1.8346
153	A	L	-0.5423
154	L	L	0.4101
155	Q	L	-0.2531
156	S	L	-0.6738
157	G	L	-1.2484
158	N	L	-1.9138
159	S	L	-1.9515
160	Q	L	-2.2768
161	E	L	-2.3507
162	S	L	-0.5348
163	V	L	0.5703
164	T	L	-0.4269
165	E	L	-2.1394
166	Q	L	-2.4622
167	D	L	-3.2249
168	S	L	-2.3935
169	K	L	-2.6772
170	D	L	-2.2341
171	S	L	-1.3973
172	T	L	0.0000
173	Y	L	-0.2560
174	S	L	0.1666
175	L	L	0.3098
176	S	L	0.3872
177	S	L	-0.6249
178	T	L	-0.8941
179	L	L	0.0000
180	T	L	-0.7713
181	L	L	0.0000
182	S	L	-0.9227
183	K	L	-1.9788
184	A	L	-1.5488
185	D	L	-1.9271
186	Y	L	-2.4680
187	E	L	-3.5640
188	K	L	-3.3041
189	H	L	-2.5869
190	K	L	-2.9687
191	V	L	-1.0615
192	Y	L	0.0000
193	A	L	-0.4768
194	C	L	0.0000
195	E	L	-0.9277
196	V	L	0.0000
197	T	L	-0.8506
198	H	L	0.0000
199	Q	L	-0.5784
200	G	L	-0.0745
201	L	L	1.1931
202	S	L	0.2567
203	S	L	0.0058
204	P	L	-0.3807
205	V	L	0.1408
206	T	L	-0.1890
207	K	L	0.0000
208	S	L	-0.0004
209	F	L	0.0000
210	N	L	-1.8248
211	R	L	-2.9420

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, -0.5933 in this case) is selected and presented in A3D results.