Project name: fab36c79e6e8e03

Status: done

Started: 2025-02-22 00:44:03
Chain sequence(s) A: MAAAGNKSINAKLVLLGDVGAGKSSLVLRFVKDQFVEFQESTIGAAFFSQTLAVNDATVKFEIWDTAGQERYHSLAPMYYRGAAAAIIVFDVTNQASFERAKKWVQELQAQGNPNMVMALAGNKSDLLDARKVTAEDAQTYAQENGLFFMETSAKTATNVKEIFYEIARRLPRVQPTENPTGMVLPDRAMDRAVSSSCCA
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:01)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:01)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:21)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/fab36c79e6e8e03/tmp/folded.pdb                (00:02:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:03)
Show buried residues
Minimal score value
-2.9697
Maximal score value
2.5567
Average score
-0.717
Total score value
-143.3901
Download the table (csv)

The table below lists A4D score for protein residues. Residues with A4D score > 0.0000 are marked by yellow rows.

residue index residue name chain Aggrescan4D score mutation
1 M A 1.1072
2 A A 0.5375
3 A A 0.0760
4 A A -0.6180
5 G A -1.4354
6 N A -2.4405
7 K A -1.9415
8 S A -1.6107
9 I A 0.0000
10 N A -1.8592
11 A A 0.0000
12 K A -1.2737
13 L A 0.0000
14 V A 0.0000
15 L A 0.0000
16 L A 0.0000
17 G A 0.0000
18 D A -0.4152
19 V A 0.6358
20 G A -0.2756
21 A A 0.0000
22 G A -0.3117
23 K A 0.0000
24 S A -0.1005
25 S A 0.0000
26 L A 0.0000
27 V A 0.0000
28 L A -0.7056
29 R A -1.7263
30 F A -1.3748
31 V A -1.1260
32 K A -2.2780
33 D A -2.8945
34 Q A -2.0188
35 F A -0.6620
36 V A 0.0778
37 E A -0.8600
38 F A 0.6916
39 Q A -0.6994
40 E A -1.5616
41 S A -0.3169
42 T A 0.4537
43 I A 1.5028
44 G A 0.7474
45 A A 1.0725
46 A A 1.2203
47 F A 1.5743
48 F A 0.9069
49 S A -0.2780
50 Q A -0.7124
51 T A -0.8145
52 L A 0.0000
53 A A -0.9705
54 V A 0.0000
55 N A -2.5486
56 D A -2.9535
57 A A 0.0000
58 T A -1.5322
59 V A 0.0000
60 K A -1.6710
61 F A 0.0000
62 E A -0.9087
63 I A 0.0000
64 W A 0.6790
65 D A 0.0000
66 T A 0.0000
67 A A 0.0000
68 G A -0.2551
69 Q A -1.2077
70 E A -2.7353
71 R A -2.6202
72 Y A -1.1738
73 H A -1.4602
74 S A -0.6160
75 L A 0.1347
76 A A 0.0000
77 P A -0.2789
78 M A 0.5115
79 Y A 0.0988
80 Y A 0.0000
81 R A -2.0083
82 G A -1.5716
83 A A 0.0000
84 A A -1.0384
85 A A 0.0000
86 A A 0.0000
87 I A 0.0000
88 I A 0.0000
89 V A 0.0000
90 F A 0.0000
91 D A 0.0000
92 V A 0.0000
93 T A -1.4345
94 N A -1.9958
95 Q A -2.3650
96 A A -1.6489
97 S A 0.0000
98 F A -1.8611
99 E A -2.7663
100 R A -1.8270
101 A A 0.0000
102 K A -2.2131
103 K A -2.4271
104 W A 0.0000
105 V A 0.0000
106 Q A -2.1277
107 E A -1.6471
108 L A 0.0000
109 Q A -2.2659
110 A A -1.3592
111 Q A -1.8358
112 G A -2.0315
113 N A -1.9126
114 P A -1.5118
115 N A -1.6972
116 M A 0.0000
117 V A -0.6243
118 M A -0.2904
119 A A 0.0000
120 L A 0.0000
121 A A 0.0000
122 G A 0.0000
123 N A 0.0000
124 K A -0.6722
125 S A -0.4582
126 D A -0.5249
127 L A 0.0683
128 L A 0.3392
129 D A -1.3399
130 A A -1.0606
131 R A -1.6241
132 K A -2.4518
133 V A 0.0000
134 T A -1.9842
135 A A -1.8933
136 E A -2.9697
137 D A -2.9289
138 A A 0.0000
139 Q A -2.5917
140 T A -2.4240
141 Y A -2.1185
142 A A 0.0000
143 Q A -2.4910
144 E A -2.7614
145 N A -2.1862
146 G A -1.5619
147 L A 0.0000
148 F A 0.0000
149 F A -0.4319
150 M A -0.2629
151 E A -0.4819
152 T A 0.0000
153 S A 0.0000
154 A A 0.0000
155 K A -1.6333
156 T A -0.8411
157 A A -1.3800
158 T A -1.0650
159 N A -1.2786
160 V A 0.0000
161 K A -2.2560
162 E A -1.8346
163 I A 0.0000
164 F A 0.0000
165 Y A -0.8003
166 E A -1.1120
167 I A 0.0000
168 A A 0.0000
169 R A -2.0085
170 R A -1.7012
171 L A 0.0000
172 P A -0.8725
173 R A -0.7839
174 V A 0.6107
175 Q A -1.0699
176 P A -1.2765
177 T A -1.5612
178 E A -2.8126
179 N A -2.3555
180 P A -1.3646
181 T A -0.5736
182 G A 0.4372
183 M A 1.9223
184 V A 2.5567
185 L A 1.7927
186 P A -0.2406
187 D A -1.9665
188 R A -2.5087
189 A A -1.6807
190 M A -1.0900
191 D A -2.2921
192 R A -2.0146
193 A A -0.4013
194 V A 0.9378
195 S A 0.3662
196 S A 0.2823
197 S A 0.3614
198 C A 0.9630
199 C A 1.0889
200 A A 0.5531
Download PDB file
View in 3Dmol

Calculations for various pH values

This page contains details and comparisons for all models calculated at different pH points.
Please find suggestions on interpreting the results below. More details can be found in the Tutorial.
The input structure is globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.3595 3.7649 View CSV PDB
4.5 -0.4317 3.7464 View CSV PDB
5.0 -0.5191 3.7186 View CSV PDB
5.5 -0.6082 3.6863 View CSV PDB
6.0 -0.6848 3.6543 View CSV PDB
6.5 -0.7374 3.628 View CSV PDB
7.0 -0.764 3.6113 View CSV PDB
7.5 -0.7717 3.6035 View CSV PDB
8.0 -0.7678 3.6006 View CSV PDB
8.5 -0.7544 3.5996 View CSV PDB
9.0 -0.7302 3.5993 View CSV PDB