Project name: 5B5 MUTANT ANTIBODY 5

Status: done

Started: 2026-03-17 05:32:03
Chain sequence(s) A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGKTYLEWYLQKPGQSPQLLIYKLSYRASGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFQGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage Used: no changes made
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:      Running AlphaCutter                                                         (00:00:02)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:11)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:12)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:12)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:55)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/d10ebdd07fe0824/tmp/folded.pdb                (00:02:55)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:45)
Show buried residues
Minimal score value
-3.1604
Maximal score value
1.7208
Average score
-0.6211
Total score value
-150.9246
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 -1.0203
2 I A 0.0000
3 V A 0.7935
4 M A 0.0000
5 T A -0.2572
6 Q A 0.0000
7 T A 0.0485
8 P A 0.4861
9 L A 1.2657
10 S A 0.1538
11 L A -0.2439
12 S A -1.1287
13 V A 0.0000
14 T A -1.6573
15 P A -1.7835
16 G A -1.6928
17 Q A -1.9096
18 P A -1.9958
19 A A 0.0000
20 S A -0.8992
21 I A 0.0000
22 S A -0.9320
23 C A 0.0000
24 R A -2.2143
25 S A 0.0000
26 S A -0.9957
27 Q A -1.5629
28 S A -0.9617
29 L A 0.0000
30 V A -0.1281
31 H A -0.8534
32 S A -0.9892
33 N A -1.5143
34 G A -1.3394
35 K A -1.6438
36 T A -0.7116
37 Y A -0.2474
38 L A 0.0000
39 E A -0.0966
40 W A 0.0000
41 Y A 0.0000
42 L A 0.0000
43 Q A -0.9349
44 K A -1.6919
45 P A -1.1265
46 G A -1.5542
47 Q A -2.1632
48 S A -1.3024
49 P A 0.0000
50 Q A -1.0977
51 L A 0.0000
52 L A 0.0000
53 I A 0.0000
54 Y A -0.0405
55 K A -0.5336
56 L A -0.3375
57 S A -0.0338
58 Y A 0.6237
59 R A -0.8663
60 A A 0.0000
61 S A -0.4940
62 G A -1.0211
63 V A 0.0000
64 P A -1.3731
65 D A -2.4468
66 R A -2.2198
67 F A 0.0000
68 S A -1.3051
69 G A -0.7434
70 S A -0.8300
71 G A -1.0905
72 S A -0.8270
73 G A -0.9405
74 T A -1.5829
75 D A -2.3520
76 F A 0.0000
77 T A -1.2244
78 L A 0.0000
79 K A -2.2478
80 I A 0.0000
81 S A -2.3551
82 R A -3.1604
83 V A 0.0000
84 E A -2.2788
85 A A -1.7401
86 E A -2.3056
87 D A 0.0000
88 V A -1.0546
89 G A 0.0000
90 V A -0.0675
91 Y A 0.0000
92 Y A 0.0000
93 C A 0.0000
94 F A 0.0000
95 Q A 0.0000
96 G A 0.2628
97 S A 0.0000
98 H A 0.2130
99 V A 1.5430
100 P A 0.7099
101 F A 0.7451
102 T A 0.4010
103 F A 0.3357
104 G A 0.0000
105 S A -0.0157
106 G A 0.0000
107 T A 0.0000
108 K A -0.4773
109 L A 0.0000
110 E A -1.7736
111 I A -1.9219
112 K A -2.3905
113 G A -1.8383
114 G A -1.7011
115 G A -1.3561
116 G A -1.2475
117 S A -1.3089
118 G A -1.5550
119 G A -1.6497
120 G A -1.6945
121 G A -1.7258
122 S A -1.0931
123 G A -1.3134
124 G A -1.2513
125 G A -1.2872
126 G A -1.1602
127 S A -0.9625
128 V A -0.8942
129 Q A -1.4244
130 L A 0.0000
131 V A -0.0880
132 Q A 0.0000
133 S A -0.7416
134 G A -0.7455
135 A A -0.2622
136 E A -0.5582
137 V A 0.6933
138 K A -0.9490
139 K A -2.0648
140 P A -2.0553
141 G A -1.4178
142 A A -1.1395
143 S A -1.2935
144 V A 0.0000
145 K A -2.1109
146 V A 0.0000
147 S A -0.7213
148 C A 0.0000
149 K A -1.2085
150 A A 0.0000
151 S A -0.7922
152 G A -0.7978
153 Y A -0.4976
154 T A -0.5836
155 F A 0.0000
156 T A -0.1164
157 D A -1.4135
158 Y A -0.6733
159 I A 0.0784
160 M A 0.0000
161 L A 0.0000
162 W A 0.0000
163 V A 0.0000
164 R A 0.0000
165 Q A -0.5840
166 A A -1.0032
167 P A -1.0127
168 G A -1.2121
169 Q A -1.6819
170 G A -0.9588
171 L A 0.0000
172 E A -0.5193
173 W A 0.0000
174 M A 0.0000
175 G A 0.0000
176 N A -0.3099
177 I A 0.0000
178 D A 0.1508
179 P A 0.0000
180 Y A 1.4055
181 Y A 1.7208
182 G A 0.4580
183 S A 0.1844
184 T A -0.1185
185 G A 0.0575
186 Y A 0.0967
187 A A 0.0000
188 L A 0.2551
189 K A -1.3854
190 F A 0.0000
191 Q A -1.4541
192 G A -1.2505
193 R A -1.2332
194 V A 0.0000
195 T A -0.8124
196 M A 0.0000
197 T A -0.5924
198 R A -0.8407
199 D A -1.2105
200 T A -0.5063
201 S A -0.5554
202 T A -0.6987
203 S A -0.8025
204 T A 0.0000
205 V A 0.0000
206 Y A -0.8014
207 M A 0.0000
208 E A -1.4796
209 L A 0.0000
210 S A -1.0652
211 S A -1.0828
212 L A 0.0000
213 R A -2.6390
214 S A -2.1668
215 E A -2.4183
216 D A 0.0000
217 T A -0.7571
218 A A 0.0000
219 V A 0.1945
220 Y A 0.0000
221 Y A 0.0000
222 C A 0.0000
223 A A 0.0000
224 R A 0.0000
225 D A -1.1875
226 G A -1.0591
227 N A -1.1763
228 Y A -0.2797
229 G A -0.5567
230 S A 0.0000
231 D A -0.6740
232 Y A -0.5747
233 W A -0.5236
234 G A 0.0000
235 Q A -1.3558
236 G A -0.5990
237 T A 0.0000
238 T A -0.0919
239 V A 0.0000
240 T A -0.3677
241 V A 0.0000
242 S A -0.8407
243 S A -0.9676
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 -0.5965 2.0354 View CSV PDB
4.5 -0.6317 1.947 View CSV PDB
5.0 -0.673 1.8378 View CSV PDB
5.5 -0.7115 1.7256 View CSV PDB
6.0 -0.7384 1.7062 View CSV PDB
6.5 -0.7482 1.6868 View CSV PDB
7.0 -0.7419 1.6675 View CSV PDB
7.5 -0.7247 1.6487 View CSV PDB
8.0 -0.7015 1.631 View CSV PDB
8.5 -0.6733 1.6151 View CSV PDB
9.0 -0.6396 1.5982 View CSV PDB