Project name: 5B5 MUTANT ANTIBODY 3

Status: done

Started: 2026-03-17 05:30:38
Chain sequence(s) A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGNTYLEWYLQKPGQPPQLLIYKLSYRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSQVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
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]                                                (00:00:00)
[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:      Running AlphaCutter                                                         (00:00:00)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:06)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:06)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:06)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:02)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/6cac1f8db8c374f/tmp/folded.pdb                (00:02:02)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:10)
Show buried residues
Minimal score value
-3.0599
Maximal score value
1.7082
Average score
-0.577
Total score value
-140.2071
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 -1.1226
2 I A 0.0000
3 V A 0.7597
4 M A 0.0000
5 T A -0.2768
6 Q A 0.0000
7 T A 0.0516
8 P A 0.4618
9 L A 1.2668
10 S A 0.1633
11 L A -0.2202
12 S A -1.0877
13 V A 0.0000
14 T A -1.5439
15 P A -1.6658
16 G A -1.5531
17 Q A -1.7890
18 P A -1.9325
19 A A 0.0000
20 S A -0.8684
21 I A 0.0000
22 S A -0.8917
23 C A 0.0000
24 R A -2.2493
25 S A 0.0000
26 S A -1.0222
27 Q A -1.6245
28 S A -0.8604
29 L A 0.0000
30 V A 0.4462
31 H A -0.5966
32 S A -0.8659
33 N A -1.5735
34 G A -0.9834
35 N A -0.7002
36 T A -0.1069
37 Y A 0.0020
38 L A 0.0000
39 E A -0.0235
40 W A 0.0000
41 Y A 0.0000
42 L A 0.0000
43 Q A 0.0000
44 K A -1.5635
45 P A -1.0512
46 G A -1.3819
47 Q A -1.7453
48 P A -1.1062
49 P A 0.0000
50 Q A -0.9098
51 L A 0.0000
52 L A 0.0000
53 I A 0.0000
54 Y A 0.1662
55 K A -0.1928
56 L A -0.0962
57 S A 0.1034
58 Y A 0.7729
59 R A -0.6162
60 F A -0.1304
61 S A -0.3254
62 G A -0.9537
63 V A -0.8937
64 P A -1.2599
65 D A -2.3981
66 R A -2.1510
67 F A 0.0000
68 S A -1.1922
69 G A -0.6379
70 S A -0.7456
71 G A -1.0299
72 S A -0.7101
73 G A -0.6887
74 T A -1.5111
75 D A -2.2481
76 F A 0.0000
77 T A -1.1596
78 L A 0.0000
79 K A -2.1393
80 I A 0.0000
81 S A -2.2917
82 R A -3.0599
83 V A 0.0000
84 E A -2.0450
85 A A -1.8751
86 E A -2.4001
87 D A 0.0000
88 V A -1.0028
89 G A 0.0000
90 V A -0.0320
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 0.0505
97 S A 0.0000
98 Q A -0.5298
99 V A 1.1500
100 P A 0.5365
101 F A 0.5701
102 T A 0.3216
103 F A 0.3392
104 G A 0.0000
105 S A -0.0127
106 G A 0.0000
107 T A 0.0000
108 K A -0.4337
109 L A 0.0000
110 E A -1.6461
111 I A -1.8771
112 K A -2.3721
113 G A -1.8354
114 G A -1.6994
115 G A -1.3497
116 G A -1.4236
117 S A -1.2574
118 G A -1.6856
119 G A -1.5582
120 G A -1.7432
121 G A -1.4780
122 S A -1.0998
123 G A -1.3663
124 G A -1.1807
125 G A -1.3058
126 G A -1.1065
127 S A -0.9573
128 V A -0.8605
129 Q A -1.2656
130 L A 0.0000
131 V A 0.2903
132 Q A 0.0000
133 S A -0.5252
134 G A -0.6201
135 A A -0.0815
136 E A -0.1670
137 V A 0.8266
138 K A -0.9727
139 K A -2.1375
140 P A -2.1398
141 G A -1.4724
142 A A -1.1829
143 S A -1.2239
144 V A 0.0000
145 K A -1.6279
146 V A 0.0000
147 S A -0.5160
148 C A 0.0000
149 K A -0.8326
150 A A 0.0000
151 S A -0.6665
152 G A -0.7924
153 Y A -0.5542
154 T A -0.4599
155 F A 0.0000
156 T A -0.1205
157 D A -1.4165
158 Y A -0.6611
159 I A 0.0943
160 M A 0.0000
161 L A 0.0000
162 W A 0.0000
163 V A 0.0000
164 R A -0.4333
165 Q A -0.6950
166 A A -1.0747
167 P A -1.0536
168 G A -1.2152
169 Q A -1.7062
170 G A -0.9862
171 L A 0.0000
172 E A -0.5934
173 W A 0.0000
174 M A 0.0000
175 G A 0.0000
176 N A -0.0045
177 I A 0.0000
178 D A 0.1443
179 P A 0.0000
180 Y A 1.3957
181 Y A 1.7082
182 G A 0.4577
183 S A 0.1447
184 T A -0.0453
185 G A 0.3989
186 Y A 0.5081
187 A A 0.0000
188 L A 0.1931
189 K A -1.5527
190 F A 0.0000
191 K A -2.0239
192 G A -1.3620
193 R A -1.2932
194 V A 0.0000
195 T A -0.5554
196 M A 0.0000
197 T A -0.6263
198 R A -0.8379
199 D A -1.1844
200 T A -0.5101
201 S A -0.5608
202 T A -0.6494
203 S A -0.7250
204 T A 0.0000
205 V A 0.0000
206 Y A -0.6932
207 M A 0.0000
208 E A -1.3021
209 L A 0.0000
210 S A -1.0113
211 S A -1.0553
212 L A 0.0000
213 R A -2.8147
214 S A -2.2618
215 E A -2.4787
216 D A 0.0000
217 T A -0.8947
218 A A 0.0000
219 V A 0.1239
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 -1.0380
226 G A -0.9315
227 N A -1.1009
228 Y A -0.0946
229 G A -0.3662
230 S A 0.0000
231 D A 0.0000
232 Y A -0.3093
233 W A -0.3581
234 G A 0.0000
235 Q A -1.1817
236 G A -0.5235
237 T A 0.0000
238 T A -0.0235
239 V A 0.0000
240 T A -0.3272
241 V A 0.0000
242 S A -0.8918
243 S A -0.9905
Download PDB file
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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 -0.5404 1.9824 View CSV PDB
4.5 -0.5725 1.8944 View CSV PDB
5.0 -0.6099 1.7876 View CSV PDB
5.5 -0.6446 1.6723 View CSV PDB
6.0 -0.6688 1.6257 View CSV PDB
6.5 -0.6776 1.607 View CSV PDB
7.0 -0.6717 1.5886 View CSV PDB
7.5 -0.656 1.5705 View CSV PDB
8.0 -0.6349 1.5642 View CSV PDB
8.5 -0.6095 1.6571 View CSV PDB
9.0 -0.5793 1.7474 View CSV PDB