Project name: 13192ee4b6b2573

Status: done

Started: 2025-03-14 20:30:43
Chain sequence(s) A: AGTYGLGD
H: VHLVESGGALVKPGGSLKLSCAASGFSFSKYGMSWVRQTPDKRLEWVATISSSGSRTYYPDSVKGQFTISRDNAKNTLYLQMSSSLKSEDTAMYYCSISWDGAMDYWGQGTSVTVSSAKTTPPSVYPLAPGSSMVTLGCCLVKGYFPEPVTVTWNSGSLSSGVHTFPAVLQSDLYTLSSSVTVPSSTWPSETVTCNVAHPASSTKVDKKIVPRD
L: DVLMTQTPLSLPVSLGDQASISCKSSQSIVHSNGNTYLEWYLQKPGQSSPKLLVYKVSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDLGTYYCFQGSLVPWAFGGGTKLEIKRADAAPTVSIFPPSSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLTLTKDEYERHNSYTCEATHKTSTSPIVKSFNRNE
input PDB
Selected Chain(s) A,H,L
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 all 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                                          (00:04:25)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/13192ee4b6b2573/tmp/folded.pdb                (00:04:25)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:14)
Show buried residues
Minimal score value
-4.0283
Maximal score value
1.4559
Average score
-0.6902
Total score value
-302.3008
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 L -1.2893
2 V L 0.0000
3 L L 0.6864
4 M L 0.0000
5 T L -0.1106
6 Q L -0.1966
7 T L 0.0689
8 P L 0.5369
9 L L 1.2953
10 S L 0.3912
11 L L 0.2248
12 P L -0.5970
13 V L 0.0000
14 S L -0.9766
15 L L -0.6832
16 G L -1.5889
17 D L -2.0947
18 Q L -2.6889
19 A L 0.0000
20 S L -0.9857
21 I L 0.0000
22 S L -0.6766
23 C L 0.0000
24 K L -1.4147
25 S L 0.0000
26 S L -0.7917
27 Q L -1.2043
28 S L -0.6380
29 I L 0.0000
30 V L 0.4110
31 H L -0.4989
32 S L -0.9319
33 N L -1.6239
34 G L -1.1221
35 N L -0.8347
36 T L -0.3027
37 Y L 0.0000
38 L L 0.0000
39 E L 0.0000
40 W L 0.0000
41 Y L 0.0000
42 L L 0.0000
43 Q L -1.1642
44 K L -1.6571
45 P L -1.2875
46 G L -1.4609
47 Q L -2.1060
48 S L -1.4149
49 P L 0.0000
50 K L -1.2875
51 L L 0.0000
52 L L 0.0000
53 V L 0.0000
54 Y L 0.0000
55 K L -1.0713
56 V L -0.7465
57 S L -1.0670
58 N L -1.5737
59 R L -1.9359
60 F L 0.0000
61 S L -0.8147
62 G L -0.9608
63 V L 0.0000
64 P L -1.4252
65 D L -2.3065
66 R L -2.3206
67 F L 0.0000
68 S L -1.6102
69 G L -1.0885
70 S L -1.0232
71 G L -0.9893
72 S L -0.6724
73 G L -0.6145
74 T L -1.1800
75 D L -1.8215
76 F L 0.0000
77 T L -1.0165
78 L L 0.0000
79 K L -2.1528
80 I L 0.0000
81 S L -2.5681
82 R L -3.0819
83 V L 0.0000
84 E L -2.0687
85 A L -1.0473
86 E L -2.0311
87 D L 0.0000
88 L L -0.5964
89 G L -0.8702
90 T L 0.0000
91 Y L 0.0000
92 Y L 0.0000
93 C L 0.0000
94 F L 0.0000
95 Q L 0.0000
96 G L 0.0000
97 S L 0.4405
98 L L 0.8921
99 V L 1.4559
100 P L 0.5938
101 W L 0.7111
102 A L 0.3561
103 F L -0.1022
104 G L 0.0000
105 G L -1.1479
106 G L 0.0000
107 T L 0.0000
108 K L -0.1484
109 L L 0.0000
110 E L 0.0000
111 I L -0.4751
112 K L -1.7510
113 R L -1.7801
114 A L -1.4367
115 D L -2.3800
116 A L -1.3134
117 A L -0.7288
118 P L 0.0000
119 T L 0.0686
120 V L 0.1765
121 S L 0.0255
122 I L 0.0000
123 F L 0.0000
124 P L -0.2938
125 P L 0.0000
126 S L 0.0000
127 S L -0.6486
128 E L -1.0912
129 Q L 0.0000
130 L L -0.9443
131 T L -0.6483
132 S L -0.6979
133 G L -1.0911
134 G L -1.0249
135 A L 0.0000
136 S L 0.0000
137 V L 0.0000
138 V L 0.0000
139 C L 0.0000
140 F L 0.0000
141 L L 0.0000
142 N L 0.0000
143 N L -0.9549
144 F L 0.0000
145 Y L 0.0000
146 P L -1.9571
147 K L -2.0483
148 D L -2.5389
149 I L 0.0000
150 N L -1.9803
151 V L -0.9815
152 K L -1.8517
153 W L 0.0000
154 K L -2.4417
155 I L 0.0000
156 D L -2.8832
157 G L -2.0567
158 S L -2.0983
159 E L -3.2451
160 R L -2.7259
161 Q L -2.4993
162 N L -2.0637
163 G L -0.9126
164 V L -0.7090
165 L L -0.1502
166 N L -0.6138
167 S L -0.2447
168 W L -0.1312
169 T L -0.9562
170 D L -2.0584
171 Q L -1.7636
172 D L -2.1681
173 S L -1.7989
174 K L -2.4275
175 D L -1.8922
176 S L -1.8829
177 T L 0.0000
178 Y L 0.0000
179 S L 0.0000
180 M L 0.0000
181 S L 0.0000
182 S L 0.0000
183 T L -0.0395
184 L L 0.0000
185 T L -0.3280
186 L L 0.0000
187 T L -1.6208
188 K L -2.7675
189 D L -3.5985
190 E L -2.9910
191 Y L 0.0000
192 E L -4.0283
193 R L -3.9228
194 H L -3.1512
195 N L -2.7889
196 S L -1.8771
197 Y L 0.0000
198 T L -1.0883
199 C L 0.0000
200 E L -0.4129
201 A L 0.0000
202 T L -1.0876
203 H L 0.0000
204 K L -2.3884
205 T L -1.3447
206 S L -0.7389
207 T L -0.5891
208 S L -0.3323
209 P L -0.3241
210 I L 0.6786
211 V L 0.8412
212 K L -0.1097
213 S L -0.4169
214 F L -1.0385
215 N L -2.1048
216 R L -2.6225
217 N L -3.0908
218 E L -3.2568
2 V H 1.2446
3 H H -0.1020
4 L H 0.0000
5 V H 0.2984
6 E H 0.0000
7 S H -0.5178
8 G H -0.7440
9 G H -0.3425
10 A H 0.1230
11 L H 0.7883
12 V H -0.4715
13 K H -1.9865
14 P H -2.0299
15 G H -1.6321
16 G H -1.1520
17 S H -1.3223
18 L H -1.1424
19 K H -2.1934
20 L H 0.0000
21 S H -0.5632
22 C H 0.0000
23 A H -0.3309
24 A H 0.0000
25 S H -0.2118
26 G H 0.0037
27 F H 0.0737
28 S H -0.5833
29 F H 0.0000
30 S H -1.2108
31 K H -1.3479
32 Y H -0.6261
33 G H 0.0000
34 M H 0.0000
35 S H 0.0000
36 W H 0.0000
37 V H 0.0000
38 R H 0.0000
39 Q H 0.0000
40 T H -2.1758
41 P H -2.1847
42 D H -3.3552
43 K H -3.6586
44 R H -3.5242
45 L H 0.0000
46 E H -1.2477
47 W H 0.0000
48 V H 0.0000
49 A H 0.0000
50 T H 0.0000
51 I H 0.0000
52 S H 0.0000
53 S H 0.0000
54 S H -1.3203
55 G H -1.0823
56 S H -1.0591
57 R H -1.0744
58 T H -0.2045
59 Y H 0.1885
60 Y H -0.5001
61 P H 0.0000
62 D H -2.4842
63 S H -1.6449
64 V H 0.0000
65 K H -2.5868
66 G H -1.7411
67 Q H -1.5803
68 F H 0.0000
69 T H -1.0109
70 I H 0.0000
71 S H -0.6379
72 R H -0.9652
73 D H -1.4605
74 N H -1.6560
75 A H -1.3109
76 K H -2.2029
77 N H -1.6640
78 T H -1.0115
79 L H 0.0000
80 Y H -0.6922
81 L H 0.0000
82 Q H -1.8420
83 M H 0.0000
84 S H -1.2248
85 S H -1.2086
86 L H 0.0000
87 K H -2.9202
88 S H -2.4279
89 E H -2.5305
90 D H 0.0000
91 T H -0.8598
92 A H 0.0000
93 M H -0.2200
94 Y H 0.0000
95 Y H 0.0000
96 C H 0.0000
97 S H 0.0000
98 I H 0.0000
99 S H 0.0000
100 W H -0.0249
101 D H -0.6968
102 G H 0.0000
103 A H 0.0000
104 M H 0.0000
105 D H 0.0000
106 Y H 0.4795
107 W H -0.1256
108 G H 0.0000
109 Q H -1.3841
110 G H 0.0000
111 T H -0.3083
112 S H -0.1748
113 V H 0.0000
114 T H -0.2994
115 V H 0.0000
116 S H -1.5431
117 S H -1.3809
118 A H -1.3704
119 K H -1.9259
120 T H -1.0666
121 T H -0.5981
122 P H -0.7328
123 P H 0.0000
124 S H -0.3091
125 V H -0.3806
126 Y H 0.0000
127 P H 0.0000
128 L H 0.0000
129 A H 0.0000
130 P H -0.2192
131 G H -1.0513
132 S H -0.6449
138 S H 0.2157
139 M H 0.8782
140 V H 0.5181
141 T H 0.3083
142 L H 0.0000
143 G H 0.0000
144 C H 0.0000
145 L H 0.0000
146 V H 0.0000
147 K H -0.3878
148 G H -0.2297
149 Y H 0.0000
150 F H 0.0000
151 P H -0.9790
152 E H -1.2917
153 P H -0.9245
154 V H -0.4571
155 T H -0.3256
156 V H -0.2141
157 T H -0.4530
158 W H 0.0000
159 N H -1.0906
160 S H -0.8724
161 G H -0.7731
162 S H -0.5692
163 L H -0.2567
164 S H -0.4059
165 S H -0.5506
166 G H -0.5461
167 V H 0.1367
168 H H -0.2433
169 T H 0.0616
170 F H 0.0000
171 P H -0.2590
172 A H 0.1955
173 V H 0.6607
174 L H 0.9737
175 Q H 0.0974
176 S H -0.4999
177 D H -1.2014
178 L H -0.4494
179 Y H 0.1036
180 T H 0.0000
181 L H 0.1612
182 S H 0.0000
183 S H 0.0000
184 S H 0.0000
185 V H 0.0000
186 T H 0.1861
187 V H 0.0000
188 P H 0.0255
189 S H -0.0328
190 S H -0.5908
191 T H -0.7936
192 W H 0.0000
193 P H -0.7317
194 S H -1.3110
195 E H -2.0623
196 T H -1.1685
197 V H 0.0000
198 T H -1.1320
199 C H 0.0000
200 N H -1.4064
201 V H 0.0000
202 A H -0.9028
203 H H 0.0000
204 P H -0.8192
205 A H -0.4467
206 S H -0.5306
207 S H -0.6964
208 T H -0.9343
209 K H -1.9530
210 V H -1.2668
211 D H -2.4830
212 K H -1.6151
213 K H -1.7437
214 I H 0.0000
215 V H 0.8918
216 P H -0.0642
217 R H -1.2985
218 D H -2.4872
15 A A -0.5977
16 G A -0.4771
17 T A -0.2501
18 Y A 0.0290
19 G A -0.4357
20 L A 0.0000
21 G A -1.2488
22 D A -2.2373
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 -0.6756 2.1986 View CSV PDB
4.5 -0.7286 2.1004 View CSV PDB
5.0 -0.7883 1.9793 View CSV PDB
5.5 -0.8444 1.9002 View CSV PDB
6.0 -0.886 1.9095 View CSV PDB
6.5 -0.9049 1.9284 View CSV PDB
7.0 -0.9025 1.957 View CSV PDB
7.5 -0.8862 1.9912 View CSV PDB
8.0 -0.861 2.0277 View CSV PDB
8.5 -0.827 2.065 View CSV PDB
9.0 -0.783 2.1024 View CSV PDB