Project name: IN011-MEDI8852-IgM

Status: done

Started: 2026-07-13 09:05:35
Chain sequence(s) A: DIQMTQSPSSLSASVGDRVTITCRTSQSLSSYTHWYQQKPGKAPKLLIYAASSRGSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQSRTFGQGTKVEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRGEC
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                                          (00:02:49)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ade0e7565db65d1/tmp/folded.pdb                (00:02:49)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:33)
Show buried residues
Minimal score value
-3.5397
Maximal score value
1.7571
Average score
-0.7439
Total score value
-156.212
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 -2.3979
2 I A -1.6092
3 Q A -1.9928
4 M A 0.0000
5 T A -1.1981
6 Q A 0.0000
7 S A -0.7646
8 P A -0.5590
9 S A -0.9385
10 S A -0.8001
11 L A -0.5123
12 S A -0.8434
13 A A 0.0000
14 S A -0.5818
15 V A 0.2422
16 G A -0.7955
17 D A -1.6232
18 R A -2.2568
19 V A 0.0000
20 T A -0.6322
21 I A 0.0000
22 T A -0.8213
23 C A 0.0000
24 R A -2.7190
25 T A 0.0000
26 S A -1.8381
27 Q A -1.8909
28 S A -0.9831
29 L A 0.2320
30 S A 0.1278
31 S A 0.2707
32 Y A 1.3348
33 T A 0.0000
34 H A 0.6831
35 W A 0.0000
36 Y A 0.1612
37 Q A 0.0000
38 Q A -1.6193
39 K A -2.0916
40 P A -1.6830
41 G A -1.6199
42 K A -2.5082
43 A A -1.4703
44 P A -1.3496
45 K A -1.5395
46 L A -0.1269
47 L A 0.0000
48 I A 0.0000
49 Y A 0.8104
50 A A 0.6106
51 A A 0.0000
52 S A -0.4039
53 S A -0.5649
54 R A -1.1823
55 G A -0.6875
56 S A -0.6554
57 G A -0.7447
58 V A 0.0000
59 P A -0.6453
60 S A -0.6872
61 R A -0.7882
62 F A 0.0000
63 S A -0.6822
64 G A -0.5068
65 S A -0.6723
66 G A -1.0901
67 S A -0.9117
68 G A -0.9852
69 T A -1.5683
70 D A -1.8300
71 F A 0.0000
72 T A -0.7409
73 L A 0.0000
74 T A -0.6009
75 I A 0.0000
76 S A -1.3103
77 S A -1.1981
78 L A 0.0000
79 Q A -0.9033
80 P A -0.7226
81 E A -1.4197
82 D A 0.0000
83 F A -0.5368
84 A A 0.0000
85 T A 0.0000
86 Y A 0.0000
87 Y A 0.0023
88 C A 0.0000
89 Q A 0.2864
90 Q A 0.0000
91 S A -0.5404
92 R A -1.7666
93 T A 0.0000
94 F A 0.8685
95 G A 0.0000
96 Q A -1.1001
97 G A 0.0000
98 T A 0.0000
99 K A -1.7972
100 V A 0.0000
101 E A 0.0000
102 I A -0.3789
103 K A -1.2682
104 R A -1.0373
105 T A -0.1186
106 V A 0.4714
107 A A -0.0224
108 A A -0.1932
109 P A 0.0000
110 S A -0.0543
111 V A 0.0000
112 F A 1.5555
113 I A 1.4310
114 F A 1.7571
115 P A 0.3873
116 P A 0.0000
117 S A -1.8080
118 D A -3.2862
119 E A -3.5397
120 Q A -2.5882
121 L A -2.6227
122 K A -3.1421
123 S A -1.9903
124 G A -1.4058
125 T A -1.1688
126 A A 0.0000
127 S A 0.0672
128 V A 0.0000
129 V A 0.8678
130 C A 0.0000
131 L A 0.8707
132 L A 0.0000
133 N A -0.4617
134 N A -1.2350
135 F A 0.0000
136 Y A 0.0000
137 P A -1.2316
138 R A -1.7649
139 E A -2.6845
140 A A -1.9069
141 K A -2.3579
142 V A -1.1060
143 Q A -0.7167
144 W A 0.0000
145 K A -0.6460
146 V A 0.0000
147 D A -1.6894
148 N A -1.4851
149 A A -0.3919
150 L A 0.3401
151 Q A -0.4668
152 S A -0.7275
153 G A -1.3660
154 N A -1.7086
155 S A -1.6990
156 Q A -2.2482
157 E A -1.7014
158 S A -0.6677
159 V A 0.4007
160 T A -0.7183
161 E A -2.0079
162 Q A -1.7601
163 D A -2.3022
164 S A -1.8574
165 K A -2.2929
166 D A -1.7098
167 S A -1.7990
168 T A 0.0000
169 Y A 0.0000
170 S A -0.6023
171 L A 0.0000
172 S A -0.0951
173 S A 0.0000
174 T A -0.6090
175 L A 0.0000
176 T A -0.6880
177 L A -0.7639
178 S A -0.9444
179 K A -1.9765
180 A A -1.6841
181 D A -2.2114
182 Y A 0.0000
183 E A -3.0862
184 K A -3.2815
185 H A -2.4797
186 K A -2.3783
187 V A -0.8514
188 Y A 0.0000
189 A A 0.0000
190 C A 0.0000
191 E A -0.7546
192 V A 0.0000
193 T A -1.2303
194 H A 0.0000
195 Q A -1.6269
196 G A -0.4015
197 L A -0.2582
198 S A -0.4560
199 S A -0.3954
200 P A -0.5991
201 V A 0.0966
202 T A -0.3519
203 K A -0.2895
204 S A -0.0885
205 F A -0.3532
206 N A -1.3423
207 R A -1.8608
208 G A -1.6511
209 E A -2.0113
210 C A -0.4209
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 -0.8416 3.7276 View CSV PDB
4.5 -0.8914 3.7278 View CSV PDB
5.0 -0.9498 3.7286 View CSV PDB
5.5 -1.0058 3.7307 View CSV PDB
6.0 -1.0465 3.7364 View CSV PDB
6.5 -1.0608 3.7483 View CSV PDB
7.0 -1.0471 3.7668 View CSV PDB
7.5 -1.0139 3.7893 View CSV PDB
8.0 -0.9695 3.8136 View CSV PDB
8.5 -0.9172 3.8384 View CSV PDB
9.0 -0.8571 3.8633 View CSV PDB