Project name: PTx S2 V1

Status: done

Started: 2025-04-27 17:18:52
Chain sequence(s) A: TPGIVIPPQEQITQHGSPYGRCANKTRALTVAELRGSGDLQEYLRHVTRGWSIFALYDGTYLGGEYGGVIKDGTPGGAFDLKTTFCIMTTRNTGQPATDHYYSNVTATRLLSSTNSRLCAVFVRSGQPVIGACTSPYDGKYVSKYEELKKKLEEVYVAGISVRVHVSKEEQYYDYEDATFETYALTGISICNPGSSLC
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]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[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                                          (00:01:29)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/14acb4e13ff612/tmp/folded.pdb                 (00:01:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:24)
Show buried residues
Minimal score value
-4.1417
Maximal score value
1.2371
Average score
-0.6713
Total score value
-132.921
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 T A -0.2418
2 P A -0.6894
3 G A -0.5184
4 I A 0.4314
5 V A 0.4188
6 I A 0.3968
7 P A 0.0000
8 P A -0.8823
9 Q A -1.8048
10 E A -2.2575
11 Q A -1.4256
12 I A 0.0000
13 T A -0.9113
14 Q A -0.9058
15 H A -1.2920
16 G A -1.2738
17 S A -0.6483
18 P A -0.3855
19 Y A 0.5485
20 G A 0.0000
21 R A -0.8264
22 C A -0.7021
23 A A -0.9651
24 N A -1.4212
25 K A -1.2642
26 T A -0.8973
27 R A 0.0000
28 A A 0.0361
29 L A 0.0000
30 T A 0.1339
31 V A 0.0000
32 A A -0.4378
33 E A 0.0000
34 L A 0.0000
35 R A -1.8663
36 G A -1.1521
37 S A 0.0000
38 G A -2.2285
39 D A -2.9977
40 L A 0.0000
41 Q A -2.4590
42 E A -3.1320
43 Y A -1.9040
44 L A 0.0000
45 R A -2.9726
46 H A -2.1322
47 V A -0.8821
48 T A 0.0000
49 R A -2.3235
50 G A -1.0057
51 W A 0.4336
52 S A 0.1372
53 I A 1.2371
54 F A 0.0000
55 A A 0.0000
56 L A 0.0000
57 Y A 0.6774
58 D A -0.9231
59 G A 0.0000
60 T A -0.5271
61 Y A 0.0000
62 L A 0.5045
63 G A 0.0000
64 G A -1.5527
65 E A -1.7210
66 Y A 0.0179
67 G A -1.0727
68 G A 0.0000
69 V A 0.5006
70 I A -0.5574
71 K A -2.1759
72 D A -2.7889
73 G A -1.7316
74 T A -1.0383
75 P A -0.5347
76 G A -0.1402
77 G A -0.3818
78 A A 0.0000
79 F A 1.0493
80 D A -0.9897
81 L A -0.5936
82 K A -1.5361
83 T A -0.9756
84 T A 0.0000
85 F A 0.0000
86 C A 0.0000
87 I A 0.0000
88 M A -0.6247
89 T A 0.0000
90 T A 0.0000
91 R A -2.8054
92 N A -2.8523
93 T A -2.0877
94 G A -1.8213
95 Q A -1.8749
96 P A -1.1610
97 A A -0.8360
98 T A -0.8049
99 D A -0.9340
100 H A -0.2086
101 Y A 0.6956
102 Y A 0.2766
103 S A -0.1845
104 N A -1.1628
105 V A 0.0000
106 T A -0.6592
107 A A 0.0000
108 T A -0.5257
109 R A -1.3609
110 L A -0.4162
111 L A 0.0000
112 S A -0.4455
113 S A 0.0000
114 T A -0.1646
115 N A -0.4495
116 S A -0.1505
117 R A 0.0000
118 L A -0.3500
119 C A 0.0000
120 A A 0.0000
121 V A 0.0000
122 F A 0.0000
123 V A -1.2354
124 R A -1.7284
125 S A -1.3579
126 G A -1.3834
127 Q A -1.7202
128 P A -1.0385
129 V A -0.5731
130 I A 0.0000
131 G A 0.0000
132 A A 0.0000
133 C A 0.0000
134 T A 0.0000
135 S A 0.0000
136 P A 0.2914
137 Y A 0.7683
138 D A -0.3186
139 G A -0.9259
140 K A -1.6360
141 Y A -0.4780
142 V A 0.1153
143 S A -0.8963
144 K A -1.8571
145 Y A 0.0000
146 E A -3.5271
147 E A -3.8293
148 L A 0.0000
149 K A -3.4008
150 K A -4.1417
151 K A -2.9606
152 L A 0.0000
153 E A -2.3037
154 E A -2.3627
155 V A 0.0000
156 Y A -0.1821
157 V A 0.8634
158 A A 0.3513
159 G A 0.1715
160 I A 0.4011
161 S A -0.3792
162 V A 0.0000
163 R A -0.0536
164 V A 0.0000
165 H A -0.0677
166 V A 0.0000
167 S A 0.0000
168 K A -1.6497
169 E A -1.9776
170 E A -2.1092
171 Q A -2.0248
172 Y A 0.0000
173 Y A -0.8051
174 D A -0.4365
175 Y A 0.0000
176 E A -1.3334
177 D A -2.0509
178 A A -1.0172
179 T A -0.9138
180 F A -0.9447
181 E A -1.8498
182 T A 0.0000
183 Y A 0.0000
184 A A 0.0000
185 L A 0.0000
186 T A -0.3453
187 G A -0.5462
188 I A 0.0000
189 S A 0.0270
190 I A 0.4627
191 C A 0.0000
192 N A -1.0907
193 P A -0.7144
194 G A -0.8437
195 S A -0.2602
196 S A 0.0613
197 L A 0.9662
198 C A 0.3016
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 -0.3632 4.4761 View CSV PDB
4.5 -0.4208 4.338 View CSV PDB
5.0 -0.4936 4.1603 View CSV PDB
5.5 -0.569 3.9677 View CSV PDB
6.0 -0.6352 3.7791 View CSV PDB
6.5 -0.6813 3.6086 View CSV PDB
7.0 -0.7023 3.4605 View CSV PDB
7.5 -0.7037 3.3281 View CSV PDB
8.0 -0.694 3.2057 View CSV PDB
8.5 -0.6769 3.0959 View CSV PDB
9.0 -0.6529 3.0117 View CSV PDB