Project name: 5B5 ORIGINAL ANTIBODY

Status: done

Started: 2026-03-17 05:40:09
Chain sequence(s) A: DIVMTQSPLSLPVSLGDQASISCRSSQSIVHSNGNTYLEWYLQKPGQSPKLLIYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGVYYCFQGSHVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLQQSGPELVKPGASVKISCKASGYSFTDYIMLWVKQSHGQSLEWIGNIDPYYGSTGYNLKFKGRATLTVDKSSSTAYMQLNSLTSEDSAVYYCARDGNYGSDYWGQGTTVTVSS
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]                                                (00:00:02)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:02)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:02)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:02)
[INFO]       PDB:      Running AlphaCutter                                                         (00:00:03)
[INFO]       PDB:      AlphaCutter did not cut any residues. The original structure will be used   
                       for analysis.                                                               (00:00:19)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:20)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:20)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:09)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/db9fa4049f650d5/tmp/folded.pdb                (00:05:09)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:06)
Show buried residues
Minimal score value
-2.9719
Maximal score value
1.7103
Average score
-0.6196
Total score value
-150.5581
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 -0.9723
2 I A 0.0000
3 V A 0.7791
4 M A 0.0000
5 T A -0.3244
6 Q A 0.0000
7 S A -0.1680
8 P A 0.3464
9 L A 1.1010
10 S A 0.1340
11 L A -0.1663
12 P A -1.0541
13 V A 0.0000
14 S A -0.8651
15 L A -0.1279
16 G A -1.3288
17 D A -2.0245
18 Q A -2.5053
19 A A 0.0000
20 S A -0.9660
21 I A 0.0000
22 S A -0.8920
23 C A 0.0000
24 R A -2.2386
25 S A 0.0000
26 S A -0.8210
27 Q A -1.1437
28 S A -0.7834
29 I A 0.0000
30 V A -0.0381
31 H A -0.7872
32 S A -1.0582
33 N A -1.7000
34 G A -1.1977
35 N A -0.9974
36 T A -0.4890
37 Y A -0.0057
38 L A 0.0000
39 E A -0.3215
40 W A 0.0000
41 Y A 0.0000
42 L A 0.0000
43 Q A 0.0000
44 K A -1.4757
45 P A -1.0770
46 G A -1.2384
47 Q A -1.6092
48 S A -1.0165
49 P A 0.0000
50 K A -1.2532
51 L A 0.0000
52 L A 0.0000
53 I A 0.0000
54 Y A -0.5508
55 K A -0.9312
56 V A -0.7658
57 S A -1.0081
58 N A -1.2321
59 R A -1.6088
60 F A -0.6347
61 S A -0.4935
62 G A -0.8091
63 V A -0.9742
64 P A -1.2111
65 D A -2.1557
66 R A -2.1255
67 F A 0.0000
68 S A -1.4206
69 G A 0.0000
70 S A -0.9694
71 G A -1.0458
72 S A -0.7996
73 G A -0.7302
74 T A -1.4010
75 D A -2.0342
76 F A 0.0000
77 T A -1.0854
78 L A 0.0000
79 K A -2.0214
80 I A 0.0000
81 S A -2.5143
82 R A -2.9719
83 V A 0.0000
84 E A -2.0356
85 A A -1.3135
86 E A -2.4604
87 D A 0.0000
88 L A -0.9894
89 G A 0.0000
90 V A -0.3790
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 0.2598
97 S A 0.0000
98 H A 0.3732
99 V A 1.5417
100 P A 0.6492
101 F A 0.6374
102 T A 0.2772
103 F A 0.0000
104 G A 0.0000
105 S A -0.1069
106 G A 0.0000
107 T A 0.0000
108 K A -0.8241
109 L A 0.0000
110 E A -1.0588
111 I A -1.0163
112 K A -1.9298
113 G A -1.6042
114 G A -1.4527
115 G A -1.3063
116 G A -1.3406
117 S A -1.0306
118 G A -1.6486
119 G A -1.5864
120 G A -1.6611
121 G A -1.5945
122 S A -1.0527
123 G A -1.3372
124 G A -1.1374
125 G A -1.1046
126 G A -0.8816
127 S A -0.7286
128 V A -0.6303
129 Q A -1.3369
130 L A 0.0000
131 Q A -2.0600
132 Q A 0.0000
133 S A -1.1595
134 G A -1.0538
135 P A -0.4117
136 E A -0.2639
137 L A 0.8846
138 V A -0.2471
139 K A -1.6308
140 P A -1.6176
141 G A -1.2904
142 A A -1.0915
143 S A -1.3525
144 V A 0.0000
145 K A -1.6519
146 I A 0.0000
147 S A -0.8158
148 C A 0.0000
149 K A -1.6518
150 A A 0.0000
151 S A -0.9122
152 G A -0.6415
153 Y A -0.4943
154 S A -0.8909
155 F A 0.0000
156 T A -0.4137
157 D A -1.4600
158 Y A -0.6873
159 I A 0.0642
160 M A 0.0000
161 L A 0.0000
162 W A 0.0000
163 V A 0.0000
164 K A -0.4229
165 Q A 0.0000
166 S A -1.2384
167 H A -1.6396
168 G A -1.3270
169 Q A -1.2833
170 S A -0.9714
171 L A 0.0000
172 E A -0.7399
173 W A 0.0000
174 I A 0.0000
175 G A 0.0000
176 N A -0.3229
177 I A 0.0000
178 D A 0.2266
179 P A 0.0000
180 Y A 1.2347
181 Y A 1.7103
182 G A 0.3400
183 S A 0.1749
184 T A -0.1494
185 G A -0.0198
186 Y A -0.0498
187 N A 0.0000
188 L A 0.0276
189 K A -1.5959
190 F A 0.0000
191 K A -1.9679
192 G A -1.6693
193 R A -1.8469
194 A A 0.0000
195 T A -0.9825
196 L A 0.0000
197 T A -0.3631
198 V A -0.5468
199 D A -1.5450
200 K A -1.8703
201 S A -1.2217
202 S A -1.0882
203 S A -1.2256
204 T A 0.0000
205 A A 0.0000
206 Y A -0.4018
207 M A 0.0000
208 Q A -1.3478
209 L A 0.0000
210 N A -1.8194
211 S A -1.2654
212 L A 0.0000
213 T A -1.3818
214 S A -1.4501
215 E A -2.0800
216 D A 0.0000
217 S A -0.7120
218 A A 0.0000
219 V A -0.0951
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 -1.1112
226 G A -0.9502
227 N A -1.0606
228 Y A -0.2674
229 G A 0.0000
230 S A 0.0000
231 D A -0.4763
232 Y A -0.2841
233 W A -0.6732
234 G A 0.0000
235 Q A -1.6860
236 G A -0.9444
237 T A 0.0000
238 T A -0.1725
239 V A 0.0000
240 T A -0.1671
241 V A 0.0000
242 S A -0.5297
243 S A -0.8694
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 -0.6695 2.0962 View CSV PDB
4.5 -0.7032 2.0519 View CSV PDB
5.0 -0.7403 1.9857 View CSV PDB
5.5 -0.7717 1.9084 View CSV PDB
6.0 -0.7886 1.8359 View CSV PDB
6.5 -0.7871 1.8159 View CSV PDB
7.0 -0.7704 1.7962 View CSV PDB
7.5 -0.7448 1.7774 View CSV PDB
8.0 -0.7142 1.761 View CSV PDB
8.5 -0.6789 1.7484 View CSV PDB
9.0 -0.6381 1.7382 View CSV PDB