Project name: ori antibody okt3

Status: done

Started: 2026-03-17 06:52:24
Chain sequence(s) A: QIVLTQSPAIMSASPGEKVTMTCSASSSVSYMNWYQQKSGTSPKRWIYDTSKLASGVPAHFRGSGSGTSYSLTISGMEAEDAATYYCQQWSSNPFTFGSGTKLEINGGGGSGGGGSGGGGSQVQLQQSGAELARPGASVKMSCKASGYTFTRYTMHWVKQRPQGLEWIGYINPSRGYTNTNQKFKDKATLTTDKSSSTAYMQLSSLTSEDSAVYYCARYYDDHYCLDYWGQGTTLTVSS
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.                                                               (00:00:21)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:22)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:22)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:13)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/51e7e829dbc576b/tmp/folded.pdb                (00:05:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:10:03)
Show buried residues
Minimal score value
-3.7222
Maximal score value
1.3031
Average score
-0.7446
Total score value
-177.9583
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 Q A -1.1155
2 I A 0.0000
3 V A 1.3031
4 L A 0.0000
5 T A 0.1838
6 Q A 0.0000
7 S A -0.0875
8 P A 0.1851
9 A A 0.4216
10 I A 0.9191
11 M A -0.0065
12 S A -1.0168
13 A A 0.0000
14 S A -1.8570
15 P A -1.9108
16 G A -2.1162
17 E A -2.7861
18 K A -2.6277
19 V A 0.0000
20 T A -0.8611
21 M A 0.0000
22 T A -0.2409
23 C A 0.0000
24 S A -0.1461
25 A A 0.0000
26 S A -0.0107
27 S A -0.3275
28 S A -0.5788
29 V A 0.0000
30 S A -0.4616
31 Y A 0.0000
32 M A 0.0000
33 N A 0.0000
34 W A 0.0000
35 Y A 0.0000
36 Q A 0.0000
37 Q A 0.0000
38 K A -1.4301
39 S A -0.7694
40 G A -0.9054
41 T A -0.9850
42 S A -0.8785
43 P A 0.0000
44 K A -1.2958
45 R A -0.6033
46 W A 0.0000
47 I A 0.0000
48 Y A -0.3886
49 D A -0.8685
50 T A -0.8486
51 S A -1.3432
52 K A -1.7491
53 L A -0.7505
54 A A 0.0000
55 S A -0.5424
56 G A -0.6400
57 V A -0.4260
58 P A -0.3570
59 A A -0.3996
60 H A -1.0997
61 F A 0.0000
62 R A -2.1301
63 G A 0.0000
64 S A -1.0353
65 G A -0.5821
66 S A -0.6062
67 G A -0.5942
68 T A -0.5589
69 S A -0.5730
70 Y A 0.0000
71 S A -0.5843
72 L A 0.0000
73 T A -1.1450
74 I A 0.0000
75 S A -1.7716
76 G A -2.0076
77 M A 0.0000
78 E A -2.7168
79 A A -2.4338
80 E A -2.8306
81 D A 0.0000
82 A A -1.9589
83 A A -1.4100
84 T A 0.0000
85 Y A 0.0000
86 Y A 0.0000
87 C A 0.0000
88 Q A 0.0000
89 Q A 0.0000
90 W A -0.1008
91 S A -0.3085
92 S A -1.0120
93 N A -1.7160
94 P A -1.4486
95 F A 0.0000
96 T A 0.0000
97 F A 0.0000
98 G A 0.0000
99 S A -0.5372
100 G A 0.0000
101 T A 0.0000
102 K A -1.4934
103 L A 0.0000
104 E A -2.2457
105 I A -2.0280
106 N A -1.5413
107 G A -1.4309
108 G A -1.5294
109 G A -1.2356
110 G A -1.2101
111 S A -1.0689
112 G A -1.6475
113 G A -1.4442
114 G A -1.6391
115 G A -1.2325
116 S A -1.3552
117 G A -1.2925
118 G A -1.2888
119 G A -1.3730
120 G A -1.4299
121 S A -1.3374
122 Q A -1.7896
123 V A 0.0000
124 Q A -2.1357
125 L A 0.0000
126 Q A -2.2245
127 Q A 0.0000
128 S A -1.1362
129 G A -0.9241
130 A A -0.1467
131 E A -0.2461
132 L A 0.7909
133 A A -0.5404
134 R A -1.8903
135 P A -1.6166
136 G A -1.1696
137 A A -0.9751
138 S A -1.1363
139 V A 0.0000
140 K A -1.9231
141 M A 0.0000
142 S A -0.9221
143 C A 0.0000
144 K A -1.7903
145 A A 0.0000
146 S A -1.1895
147 G A -0.9224
148 Y A -0.5729
149 T A -0.6714
150 F A 0.0000
151 T A -1.5437
152 R A -1.9081
153 Y A -0.9124
154 T A -0.4250
155 M A 0.0000
156 H A 0.0000
157 W A 0.0000
158 V A 0.0000
159 K A 0.0000
160 Q A -0.7603
161 R A -1.4218
162 P A -1.1110
163 Q A -1.6984
164 G A -1.1620
165 L A 0.0000
166 E A -1.1900
167 W A 0.0000
168 I A 0.0000
169 G A 0.0000
170 Y A -0.0690
171 I A 0.0000
172 N A -0.8088
173 P A 0.0000
174 S A -1.5668
175 R A -1.7294
176 G A -1.0822
177 Y A 0.1495
178 T A -0.3419
179 N A -1.3702
180 T A -1.8967
181 N A 0.0000
182 Q A -3.0791
183 K A -3.1815
184 F A 0.0000
185 K A -3.7222
186 D A -3.2766
187 K A -2.2917
188 A A 0.0000
189 T A -1.2251
190 L A 0.0000
191 T A -0.3500
192 T A -1.0817
193 D A -1.8542
194 K A -2.3025
195 S A -1.3390
196 S A -1.1951
197 S A -1.3168
198 T A 0.0000
199 A A 0.0000
200 Y A -0.5895
201 M A 0.0000
202 Q A -1.3658
203 L A 0.0000
204 S A -1.1376
205 S A -1.0246
206 L A 0.0000
207 T A -1.3400
208 S A -1.4971
209 E A -2.0309
210 D A 0.0000
211 S A -0.6623
212 A A 0.0000
213 V A 0.0700
214 Y A 0.0000
215 Y A 0.0000
216 C A 0.0000
217 A A 0.0000
218 R A 0.0000
219 Y A 0.0000
220 Y A -1.0352
221 D A -2.3990
222 D A -2.4590
223 H A -1.4233
224 Y A -0.3545
225 C A 0.0000
226 L A 0.0000
227 D A 0.0000
228 Y A -0.1921
229 W A -0.6439
230 G A 0.0000
231 Q A -1.6456
232 G A -0.8193
233 T A 0.0000
234 T A -0.0503
235 L A 0.0000
236 T A -0.2051
237 V A 0.0000
238 S A -0.6735
239 S A -0.9803
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 -0.8001 1.5667 View CSV PDB
4.5 -0.8328 1.52 View CSV PDB
5.0 -0.873 1.4558 View CSV PDB
5.5 -0.9123 1.3916 View CSV PDB
6.0 -0.9404 1.354 View CSV PDB
6.5 -0.949 1.3772 View CSV PDB
7.0 -0.9373 1.4777 View CSV PDB
7.5 -0.912 1.6349 View CSV PDB
8.0 -0.8797 1.8187 View CSV PDB
8.5 -0.8431 2.0123 View CSV PDB
9.0 -0.8026 2.2084 View CSV PDB