Project name: qTIMs

Status: done

Started: 2025-07-30 18:33:18
Chain sequence(s) A: DVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDATDVDEMLKQVEILRRLGAKQIAVRSDDWRILQEALKKGGDILIVDAT
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.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:37)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/73bf89365585b34/tmp/folded.pdb                (00:05:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:08:27)
Show buried residues
Minimal score value
-2.8565
Maximal score value
0.0
Average score
-1.1856
Total score value
-218.1415
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 D A -2.2348
2 V A -1.8076
3 D A -2.6580
4 E A -2.5130
5 M A 0.0000
6 L A -1.8995
7 K A -2.1049
8 Q A 0.0000
9 V A 0.0000
10 E A -1.9680
11 I A -1.2959
12 L A 0.0000
13 R A -2.2422
14 R A -2.1839
15 L A -0.9337
16 G A -1.2625
17 A A 0.0000
18 K A -2.2808
19 Q A -1.5155
20 I A 0.0000
21 A A 0.0000
22 V A 0.0000
23 R A -1.0009
24 S A 0.0000
25 D A -2.3108
26 D A -1.7165
27 W A -1.5790
28 R A -2.0228
29 I A -1.5074
30 L A 0.0000
31 Q A -1.4447
32 E A -1.9906
33 A A 0.0000
34 L A -1.5608
35 K A -2.2845
36 K A -2.2599
37 G A -1.5337
38 G A 0.0000
39 D A -1.6283
40 I A 0.0000
41 L A 0.0000
42 I A 0.0000
43 V A 0.0000
44 D A -1.4846
45 A A -1.8889
46 T A -1.5538
47 D A -2.1081
48 V A -1.8058
49 D A -2.7772
50 E A -2.8565
51 M A 0.0000
52 L A -2.0139
53 K A -2.3638
54 Q A 0.0000
55 V A 0.0000
56 E A -1.9337
57 I A -1.1577
58 L A 0.0000
59 R A -2.2027
60 R A -2.1196
61 L A -0.8897
62 G A -1.0930
63 A A 0.0000
64 K A -2.2402
65 Q A -1.4437
66 I A 0.0000
67 A A 0.0000
68 V A 0.0000
69 R A -0.9457
70 S A -1.5342
71 D A -2.3411
72 D A -1.6904
73 W A -1.5933
74 R A -1.9971
75 I A -1.3725
76 L A 0.0000
77 Q A -1.4407
78 E A -1.9339
79 A A 0.0000
80 L A -1.4809
81 K A -2.2688
82 K A -2.1997
83 G A -1.4110
84 G A 0.0000
85 D A -1.2312
86 I A 0.0000
87 L A 0.0000
88 I A 0.0000
89 V A 0.0000
90 D A -1.4817
91 A A -1.6961
92 T A -1.4181
93 D A -1.8946
94 V A -1.5421
95 D A -2.4445
96 E A -2.3225
97 M A 0.0000
98 L A -1.8540
99 K A -2.0785
100 Q A 0.0000
101 V A 0.0000
102 E A -2.2391
103 I A -1.5071
104 L A 0.0000
105 R A -2.4551
106 R A -2.3647
107 L A -1.0967
108 G A -1.5490
109 A A 0.0000
110 K A -2.3348
111 Q A -1.5644
112 I A 0.0000
113 A A 0.0000
114 V A 0.0000
115 R A -1.0417
116 S A -1.4414
117 D A -2.3169
118 D A -1.6548
119 W A -1.5505
120 R A -1.9729
121 I A -1.3278
122 L A 0.0000
123 Q A -1.4066
124 E A -1.8861
125 A A 0.0000
126 L A -1.5146
127 K A -2.2641
128 K A -2.2888
129 G A -1.5833
130 G A 0.0000
131 D A -1.6908
132 I A 0.0000
133 L A 0.0000
134 I A 0.0000
135 V A 0.0000
136 D A -1.5195
137 A A -1.7983
138 T A -1.4616
139 D A -1.9604
140 V A -1.6103
141 D A -2.4941
142 E A -2.3620
143 M A 0.0000
144 L A -1.9021
145 K A -2.1306
146 Q A 0.0000
147 V A 0.0000
148 E A -2.2108
149 I A -1.4445
150 L A 0.0000
151 R A -2.3531
152 R A -2.2606
153 L A -0.9660
154 G A -1.1162
155 A A 0.0000
156 K A -2.3488
157 Q A -1.6622
158 I A 0.0000
159 A A 0.0000
160 V A 0.0000
161 R A -1.2931
162 S A 0.0000
163 D A -2.3382
164 D A -1.7086
165 W A -1.5736
166 R A -1.9719
167 I A -1.3825
168 L A 0.0000
169 Q A -1.4063
170 E A -1.8881
171 A A 0.0000
172 L A -1.5307
173 K A -2.2835
174 K A -2.2931
175 G A -1.5765
176 G A 0.0000
177 D A -1.6115
178 I A 0.0000
179 L A 0.0000
180 I A 0.0000
181 V A 0.0000
182 D A -1.3259
183 A A 0.0000
184 T A -1.4600
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 -1.2435 0.3844 View CSV PDB
4.5 -1.3677 0.0 View CSV PDB
5.0 -1.5086 0.0 View CSV PDB
5.5 -1.6488 0.0 View CSV PDB
6.0 -1.7696 0.0 View CSV PDB
6.5 -1.8537 0.0 View CSV PDB
7.0 -1.8994 0.0 View CSV PDB
7.5 -1.9193 0.0 View CSV PDB
8.0 -1.9226 0.0 View CSV PDB
8.5 -1.9069 0.0 View CSV PDB
9.0 -1.8646 0.0 View CSV PDB