Project name: 96fcd9020f24b49

Status: done

Started: 2025-03-31 15:55:48
Chain sequence(s) O: DIQMTQSPSTLSASVGDRVTITCRSSQSIVHSNGNTYLEWYQQKPGKAPKLLIYKVSNRFSGVPARFSGSGSGTEFTLTISSLQPDDFATYYCFQGSHVPRTFGQGTKVEVKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG
N: QVQLVQSGAEVKKPGSSVKVSCKASGYTFTSYHIHWVRQAPGQGLEWIGWIYPGNVNTEYNEKFKGKATITADESTNTAYMELSSLRSEDTAVYYCAREEITYAMDYWGQGTLVTVSSASTKGPSVFPLAPSSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKKVEPK
input PDB
Selected Chain(s) N,O
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]                                                (00:00:01)
[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 all chain(s) selected           (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:06:43)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/96fcd9020f24b49/tmp/folded.pdb                (00:06:43)
[INFO]       Main:     Simulation completed successfully.                                          (00:11:22)
Show buried residues
Minimal score value
-3.6542
Maximal score value
1.9476
Average score
-0.7417
Total score value
-320.4261
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 N -1.4880
2 V N -1.0106
3 Q N -1.7271
4 L N 0.0000
5 V N -0.7832
6 Q N 0.0000
7 S N -0.5078
8 G N -0.6498
9 A N -0.4900
10 E N -1.6584
11 V N -0.9852
12 K N -1.7403
13 K N -2.3965
14 P N -2.2105
15 G N -1.6462
16 S N -1.2342
17 S N -1.3897
18 V N -0.9685
19 K N -1.7555
20 V N 0.0000
21 S N -0.7667
22 C N 0.0000
23 K N -1.9176
24 A N 0.0000
25 S N -1.2447
26 G N -0.9945
27 Y N -0.4121
28 T N -0.3084
29 F N 0.0000
30 T N -0.8320
31 S N -0.0486
32 Y N 0.4250
33 H N 0.2829
34 I N 0.0000
35 H N 0.0000
36 W N 0.0000
37 V N 0.0000
38 R N -0.2085
39 Q N -0.3830
40 A N -0.8125
41 P N -0.6704
42 G N -1.0444
43 Q N -1.2492
44 G N -1.0262
45 L N 0.0000
46 E N -0.6139
47 W N 0.0000
48 I N 0.0000
49 G N 0.0000
50 W N -0.0297
51 I N 0.0000
52 Y N -0.1015
53 P N 0.0000
54 G N -1.3482
55 N N -1.2811
56 V N -0.1085
57 N N -1.1315
58 T N -0.7492
59 E N -1.2052
60 Y N -1.4786
61 N N 0.0000
62 E N -3.3338
63 K N -3.2860
64 F N 0.0000
65 K N -3.4649
66 G N -2.4854
67 K N -2.8599
68 A N 0.0000
69 T N -1.1571
70 I N 0.0000
71 T N -0.1050
72 A N -1.1117
73 D N -2.2837
74 E N -2.7936
75 S N -1.6568
76 T N -1.6397
77 N N -2.0739
78 T N 0.0000
79 A N 0.0000
80 Y N -0.5013
81 M N 0.0000
82 E N -1.4213
83 L N 0.0000
84 S N -1.4530
85 S N -1.4885
86 L N 0.0000
87 R N -3.1272
88 S N -2.3972
89 E N -2.6606
90 D N -1.7270
91 T N -0.8080
92 A N 0.0000
93 V N 0.5635
94 Y N 0.0000
95 Y N 0.0000
96 C N 0.0000
97 A N 0.0000
98 R N 0.0000
99 E N 0.0000
100 E N 0.7744
101 I N 1.9476
102 T N 0.8819
103 Y N 0.8425
104 A N 0.0000
105 M N 0.0000
106 D N 0.0000
107 Y N -0.3500
108 W N -0.4172
109 G N 0.0000
110 Q N -1.4537
111 G N -0.5924
112 T N 0.0000
113 L N 1.0652
114 V N 0.5742
115 T N -0.8040
116 V N 0.0000
117 S N -1.2733
118 S N -1.2259
119 A N -0.6433
120 S N -0.7098
121 T N -0.9585
122 K N -1.3406
123 G N -1.4865
124 P N 0.0000
125 S N -0.2504
126 V N 0.0000
127 F N 0.0000
128 P N -1.0690
129 L N 0.0000
130 A N -1.2008
131 P N 0.0000
132 S N -0.6171
133 S N -0.5679
138 G N -0.7818
139 G N -0.8271
140 T N -0.5511
141 A N -0.2914
142 A N 0.0000
143 L N 0.0000
144 G N 0.0000
145 C N 0.0000
146 L N 0.0000
147 V N 0.0000
148 K N 0.0000
149 D N -0.5434
150 Y N 0.0000
151 F N 0.0000
152 P N -1.4882
153 E N -1.7036
154 P N -1.3980
155 V N -0.8555
156 T N -0.4227
157 V N -0.0085
158 S N -0.1894
159 W N 0.0000
160 N N -0.7348
161 S N -0.7137
162 G N -0.6231
163 A N -0.2961
164 L N -0.0967
165 T N -0.2190
166 S N -0.1478
167 G N -0.1143
168 V N 0.1936
169 H N -0.2538
170 T N -0.1468
171 F N 0.0000
172 P N -0.4160
173 A N -0.1833
174 V N 0.2676
175 L N 0.7906
176 Q N 0.1411
177 S N -0.0941
178 S N -0.2409
179 G N -0.0398
180 L N -0.1373
181 Y N 0.0000
182 S N -0.2104
183 L N 0.0000
184 S N 0.0000
185 S N 0.0000
186 V N 0.0000
187 V N 0.0000
188 T N -0.0651
189 V N -0.0373
190 P N -0.4572
191 S N -0.6101
192 S N -0.5888
193 S N -0.6405
194 L N -0.8146
195 G N -1.0612
196 T N -0.8573
197 Q N -1.4966
198 T N -1.1883
199 Y N 0.0000
200 I N -1.0473
201 C N 0.0000
202 N N -1.3582
203 V N 0.0000
204 N N -1.8051
205 H N 0.0000
206 K N -2.8519
207 P N -2.0973
208 S N -1.8860
209 N N -2.6699
210 T N -2.1542
211 K N -2.6561
212 V N -1.6407
213 D N -2.3861
214 K N -1.8688
215 K N -2.0036
216 V N 0.0000
217 E N -2.6496
218 P N -1.8395
219 K N -2.2033
1 D O -2.0429
2 I O 0.0000
3 Q O -1.9849
4 M O 0.0000
5 T O -1.0968
6 Q O 0.0000
7 S O -0.4783
8 P O -0.3764
9 S O -0.5960
10 T O -0.4255
11 L O -0.3150
12 S O -0.7128
13 A O 0.0000
14 S O -0.2788
15 V O 0.5571
16 G O -0.5165
17 D O -1.2974
18 R O -2.1115
19 V O 0.0000
20 T O -0.5593
21 I O 0.0000
22 T O -0.7821
23 C O 0.0000
24 R O -2.0600
25 S O 0.0000
26 S O -1.8328
27 Q O -2.1261
28 S O -1.1219
29 I O 0.0000
30 V O -0.3937
31 H O -0.9778
32 S O -1.1734
33 N O -1.7943
34 G O -1.4228
35 N O -1.3508
36 T O -0.7584
37 Y O 0.0000
38 L O 0.0000
39 E O 0.0000
40 W O 0.0000
41 Y O 0.0000
42 Q O 0.0000
43 Q O 0.0000
44 K O -2.1058
45 P O -1.6269
46 G O -1.7125
47 K O -2.7052
48 A O -1.7938
49 P O 0.0000
50 K O -1.7613
51 L O 0.0000
52 L O 0.0000
53 I O 0.0000
54 Y O -0.4471
55 K O -0.8437
56 V O 0.0000
57 S O -1.0372
58 N O -1.3240
59 R O -1.5403
60 F O -0.8236
61 S O -0.6634
62 G O -0.7040
63 V O 0.0000
64 P O -0.5033
65 A O -0.4705
66 R O -0.8458
67 F O 0.0000
68 S O -0.7480
69 G O -0.7452
70 S O -0.9472
71 G O -1.1676
72 S O -1.1134
73 G O -1.0058
74 T O -1.6707
75 E O -2.5645
76 F O 0.0000
77 T O -0.8206
78 L O 0.0000
79 T O -0.6211
80 I O 0.0000
81 S O -1.3145
82 S O -0.9330
83 L O 0.0000
84 Q O -0.8973
85 P O -0.9333
86 D O -1.9453
87 D O 0.0000
88 F O -0.5030
89 A O 0.0000
90 T O -0.6193
91 Y O 0.0000
92 Y O 0.0000
93 C O 0.0000
94 F O 0.0000
95 Q O 0.0000
96 G O 0.2229
97 S O 0.0000
98 H O -0.1334
99 V O 0.8503
100 P O -0.0833
101 R O 0.0000
102 T O -0.4360
103 F O 0.0000
104 G O 0.0000
105 Q O -1.2891
106 G O -0.7675
107 T O 0.0000
108 K O -0.8298
109 V O 0.0000
110 E O 0.0000
111 V O -0.4704
112 K O -1.3836
113 R O -1.3263
114 T O -0.2798
115 V O 0.2078
116 A O 0.1093
117 A O -0.1125
118 P O 0.0000
119 S O -0.1723
120 V O 0.0000
121 F O 0.0000
122 I O 0.0000
123 F O 0.0000
124 P O -0.6359
125 P O -0.8198
126 S O -1.9018
127 D O -3.0474
128 E O -3.2056
129 Q O 0.0000
130 L O -2.3972
131 K O -2.8152
132 S O -1.7258
133 G O -1.4032
134 T O -0.9649
135 A O 0.0000
136 S O 0.0000
137 V O 0.0000
138 V O 0.0000
139 C O 0.0000
140 L O 0.0000
141 L O 0.0000
142 N O 0.0000
143 N O -0.6567
144 F O 0.0000
145 Y O 0.0000
146 P O -1.8144
147 R O -3.1040
148 E O -3.3022
149 A O -2.3834
150 K O -2.3455
151 V O -1.1729
152 Q O -0.6288
153 W O 0.0000
154 K O -0.5334
155 V O 0.0000
156 D O -1.8570
157 N O -1.4899
158 A O -0.2696
159 L O 0.6259
160 Q O -0.1729
161 S O -0.4841
162 G O -0.9801
163 N O -1.0169
164 S O -1.2643
165 Q O -1.4352
166 E O -1.9356
167 S O -0.9672
168 V O -0.7149
169 T O -1.0948
170 E O -2.2462
171 Q O -1.9048
172 D O -1.9806
173 S O -1.7774
174 K O -2.3623
175 D O -1.9232
176 S O -1.8506
177 T O 0.0000
178 Y O 0.0000
179 S O 0.0000
180 L O 0.0000
181 S O 0.0000
182 S O 0.0000
183 T O -0.7307
184 L O 0.0000
185 T O -0.5370
186 L O 0.0000
187 S O -1.2224
188 K O -2.2331
189 A O -1.9973
190 D O -2.6875
191 Y O 0.0000
192 E O -3.6014
193 K O -3.6542
194 H O -2.9798
195 K O -2.8577
196 V O -1.2756
197 Y O 0.0000
198 A O 0.0000
199 C O 0.0000
200 E O -0.6898
201 V O 0.0000
202 T O -1.1943
203 H O 0.0000
204 Q O -1.6525
205 G O -0.5073
206 L O -0.4023
207 S O -0.4982
208 S O -0.4089
209 P O -0.4638
210 V O -0.0080
211 T O -0.5225
212 K O -0.7892
213 S O -0.6828
214 F O -0.8697
215 N O -1.8972
216 R O -2.1860
217 G O -1.2193
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 -0.8036 2.8684 View CSV PDB
4.5 -0.8493 2.8623 View CSV PDB
5.0 -0.9042 2.8474 View CSV PDB
5.5 -0.9563 2.8205 View CSV PDB
6.0 -0.9925 2.7836 View CSV PDB
6.5 -1.0018 2.7414 View CSV PDB
7.0 -0.983 2.6993 View CSV PDB
7.5 -0.9456 2.6655 View CSV PDB
8.0 -0.8987 2.6456 View CSV PDB
8.5 -0.8458 2.6368 View CSV PDB
9.0 -0.7877 2.6331 View CSV PDB