Project name: BAP C-region

Status: done

Started: 2025-11-12 22:12:15
Chain sequence(s) A: TAPDAPTVNDVTSNDKVINGTAEPNSTVKLTFPDGTTAAGTTDSNGNYTVDIPENMSLKGGETITATSSDAEGNESESATTTVVDATAPDAPTVNDVTSDATQVTGQAEPNSTVTVTFPDGTTATGTADDQGNYTIDIPSNVDLNGGEELQVTATDKDGNTSEPSSANVTDT
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                                          (00:02:19)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/5cd17a28d8e087f/tmp/folded.pdb                (00:02:19)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:51)
Show buried residues
Minimal score value
-4.177
Maximal score value
0.0
Average score
-1.469
Total score value
-252.6611
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 -0.4179
2 A A -1.5472
3 P A -2.5156
4 D A -2.8804
5 A A -1.9345
6 P A 0.0000
7 T A -0.9697
8 V A -1.0960
9 N A -2.2247
10 D A -2.2605
11 V A 0.0000
12 T A -1.2607
13 S A 0.0000
14 N A -2.0634
15 D A -2.2194
16 K A -2.7380
17 V A -1.7005
18 I A 0.0000
19 N A -1.6702
20 G A 0.0000
21 T A -1.7052
22 A A 0.0000
23 E A -3.3945
24 P A -3.0601
25 N A -3.0036
26 S A 0.0000
27 T A -1.4530
28 V A 0.0000
29 K A -1.0680
30 L A 0.0000
31 T A -0.7547
32 F A 0.0000
33 P A -1.3911
34 D A -2.1542
35 G A -1.4672
36 T A -1.0675
37 T A -0.6599
38 A A -0.6391
39 A A -0.6496
40 G A -1.1520
41 T A -1.4670
42 T A 0.0000
43 D A -3.5026
44 S A -2.6404
45 N A -2.9268
46 G A 0.0000
47 N A -2.9970
48 Y A 0.0000
49 T A -1.1321
50 V A 0.0000
51 D A -2.4445
52 I A 0.0000
53 P A -2.0769
54 E A -2.9417
55 N A -2.1835
56 M A -2.0647
57 S A -1.6606
58 L A 0.0000
59 K A -2.1532
60 G A -1.4245
61 G A -0.8618
62 E A -0.9904
63 T A -0.3377
64 I A 0.0000
65 T A -0.5034
66 A A 0.0000
67 T A -1.3850
68 S A 0.0000
69 S A -2.6359
70 D A -2.8465
71 A A -1.8180
72 E A -2.6565
73 G A -2.2618
74 N A -2.7255
75 E A -3.1281
76 S A -2.7084
77 E A -2.6626
78 S A -1.6108
79 A A -0.6874
80 T A -0.4257
81 T A -0.5949
82 T A -0.3621
83 V A 0.0000
84 V A -0.0004
85 D A -1.5390
86 A A -0.9994
87 T A -1.2880
88 A A -1.7498
89 P A 0.0000
90 D A -2.3502
91 A A -1.7867
92 P A 0.0000
93 T A -1.3593
94 V A -1.3158
95 N A -2.3959
96 D A -2.6222
97 V A 0.0000
98 T A -2.4041
99 S A -2.5100
100 D A -2.7260
101 A A -2.0902
102 T A -1.6953
103 Q A -2.2938
104 V A 0.0000
105 T A -1.7141
106 G A -1.6397
107 Q A -2.5014
108 A A -2.4497
109 E A -2.6513
110 P A -3.1596
111 N A -3.2799
112 S A 0.0000
113 T A -1.1573
114 V A 0.0000
115 T A -0.1890
116 V A 0.0000
117 T A -0.8898
118 F A 0.0000
119 P A -2.2213
120 D A -2.2583
121 G A -1.5018
122 T A -0.8277
123 T A -0.5681
124 A A -0.4661
125 T A -0.4131
126 G A -0.9378
127 T A -1.3566
128 A A 0.0000
129 D A -4.1770
130 D A -3.9874
131 Q A -3.5949
132 G A 0.0000
133 N A -3.4354
134 Y A 0.0000
135 T A -1.4375
136 I A 0.0000
137 D A -2.3258
138 I A 0.0000
139 P A -1.4608
140 S A -1.4921
141 N A -1.5929
142 V A -1.4021
143 D A -2.4426
144 L A 0.0000
145 N A -2.8805
146 G A -2.6622
147 G A -2.2382
148 E A -2.9677
149 E A -2.6132
150 L A 0.0000
151 Q A -1.0812
152 V A 0.0000
153 T A -0.9111
154 A A 0.0000
155 T A -1.8046
156 D A -2.5535
157 K A -3.2619
158 D A -3.0018
159 G A -2.2298
160 N A -1.6154
161 T A -1.4934
162 S A -1.7507
163 E A -2.3080
164 P A -1.4677
165 S A -0.9179
166 S A -0.8820
167 A A -1.8068
168 N A -2.8436
169 V A 0.0000
170 T A -2.4653
171 D A -2.8673
172 T A -1.4437
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 -0.36 1.9008 View CSV PDB
4.5 -0.5095 1.7324 View CSV PDB
5.0 -0.6889 1.5231 View CSV PDB
5.5 -0.8773 1.2979 View CSV PDB
6.0 -1.0575 1.0712 View CSV PDB
6.5 -1.2172 0.8497 View CSV PDB
7.0 -1.352 0.6335 View CSV PDB
7.5 -1.4665 0.4216 View CSV PDB
8.0 -1.5654 0.3776 View CSV PDB
8.5 -1.6449 0.3772 View CSV PDB
9.0 -1.6948 0.3771 View CSV PDB