Project name: 28ba17c2b95e1da

Status: done

Started: 2025-05-15 10:38:51
Chain sequence(s) A: SKGEELFTGVVPILVELDGDVNGHKFSVSGEGEGDATYGKLTLKFICTTGKLPVPWPTLVTTFVQCFSRYPDHKRHDFFKSAPEGYVQERTIFFKDDGNYKTRAEVKFEGDTLVNRIELKGIDFKEDGNILGHKLEYNYNSHNVYIADKQKNGIKVNFKIRHNIEDGSVQLADHYQQNTPIGDGPVLLPDNHYLSTQSALSKDPNEKRDHVLLEFVTAAGI
input PDB
Selected Chain(s) A
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 A 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                                          (00:04:01)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/28ba17c2b95e1da/tmp/folded.pdb                (00:04:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:22)
Show buried residues
Minimal score value
-4.0025
Maximal score value
1.3023
Average score
-0.9402
Total score value
-207.7815
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
2 S A -1.6232
3 K A -1.8344
4 G A 0.0000
5 E A -2.4158
6 E A -2.4813
7 L A -1.1449
8 F A 0.0000
9 T A -0.5715
10 G A 0.4722
11 V A 1.3023
12 V A 0.0000
13 P A -0.9548
14 I A 0.0000
15 L A -1.2196
16 V A 0.0000
17 E A -2.0055
18 L A 0.0000
19 D A -3.3638
20 G A 0.0000
21 D A -2.3746
22 V A 0.0000
23 N A -1.9172
24 G A -1.5229
25 H A -2.0162
26 K A -2.7753
27 F A 0.0000
28 S A -1.6500
29 V A 0.0000
30 S A -1.0404
31 G A 0.0000
32 E A -2.2774
33 G A -1.5688
34 E A -1.5111
35 G A 0.0000
36 D A 0.2222
37 A A 0.0000
38 T A 0.3532
39 Y A 1.0542
40 G A 0.0000
41 K A -0.1694
42 L A 0.0000
43 T A -0.6983
44 L A 0.0000
45 K A -1.1839
46 F A 0.0000
47 I A -1.0799
48 C A 0.0000
49 T A -0.7772
50 T A -1.2956
51 G A -1.6060
52 K A -2.2516
53 L A 0.0000
54 P A -1.1504
55 V A 0.0000
56 P A 0.0000
57 W A 0.0231
58 P A 0.0000
59 T A 0.0000
60 L A 0.0000
61 V A 0.2486
62 T A 0.0923
63 T A 0.0000
64 F A 0.0000
68 V A -0.0253
69 Q A -0.1858
70 C A 0.0000
71 F A 0.0000
72 S A 0.0000
73 R A -0.9877
74 Y A 0.0000
75 P A -1.7258
76 D A -2.9968
77 H A -2.2185
79 K A -3.0582
80 R A -2.8974
81 H A -1.6365
82 D A 0.0000
83 F A 0.0000
84 F A 0.0000
85 K A -1.0437
86 S A 0.0000
87 A A 0.0000
89 P A -1.8358
90 E A -2.5014
91 G A 0.0000
92 Y A 0.0000
93 V A -0.8085
94 Q A -1.4130
95 E A -1.9491
96 R A 0.0000
97 T A -0.3196
98 I A 0.0000
99 F A 0.3448
100 F A 0.0000
101 K A -1.5656
102 D A -2.5549
103 D A -2.5301
104 G A 0.0000
105 N A -0.7690
106 Y A 0.0000
107 K A -1.7841
108 T A 0.0000
109 R A -2.8055
110 A A 0.0000
111 E A -2.1859
112 V A 0.0000
113 K A -2.0125
114 F A -2.0043
115 E A -2.7788
116 G A -2.2850
117 D A -2.5431
118 T A -1.7526
119 L A 0.0000
120 V A 0.0000
121 N A 0.0000
122 R A -3.1369
123 I A 0.0000
124 E A -3.9010
125 L A 0.0000
126 K A -2.6838
127 G A 0.0000
128 I A -1.1782
129 D A -2.2986
130 F A 0.0000
131 K A -3.9986
132 E A -4.0025
133 D A -3.6333
134 G A -2.8364
135 N A -2.1737
136 I A 0.0000
137 L A -1.9455
138 G A -2.3148
139 H A -2.2197
140 K A -2.5171
141 L A 0.0000
142 E A -1.8052
143 Y A -0.5803
144 N A -0.5425
145 Y A -0.6452
146 N A -0.9683
147 S A -1.1297
148 H A 0.0000
149 N A -1.3544
150 V A 0.0000
151 Y A 0.1591
152 I A 0.0000
154 A A -2.0168
155 D A 0.0000
156 K A -3.2555
157 Q A -3.1524
158 K A -3.5128
159 N A -2.6934
160 G A 0.0000
161 I A 0.0000
162 K A -2.2183
163 V A 0.0000
164 N A -0.7970
165 F A 0.0000
166 K A -1.3196
167 I A 0.0000
168 R A -0.8995
169 H A 0.0000
170 N A -1.1764
171 I A 0.0000
172 E A -3.2773
173 D A -2.9946
174 G A -1.8246
175 S A -0.7602
176 V A 0.3008
177 Q A 0.0000
178 L A -0.4196
179 A A 0.0000
180 D A 0.0000
181 H A 0.0000
182 Y A 0.1409
183 Q A 0.0000
184 Q A -1.4652
185 N A 0.0000
186 T A -0.9647
187 P A -0.9383
188 I A -0.5482
189 G A -1.3958
190 D A -2.0605
191 G A -1.3898
192 P A -0.8035
193 V A -0.4859
194 L A -0.4343
195 L A -0.7420
196 P A 0.0000
197 D A -2.2553
198 N A -1.7139
199 H A 0.0000
200 Y A 0.1748
201 L A 0.0000
202 S A -0.6574
203 T A -0.8901
204 Q A -1.2935
205 S A -0.4580
206 A A 0.0700
207 L A 0.0913
208 S A -0.5911
209 K A -1.6633
210 D A -2.1036
211 P A -1.7907
212 N A -2.4583
213 E A -2.7088
214 K A -3.1931
215 R A -3.3977
216 D A -2.2888
217 H A 0.0000
219 V A -0.1042
220 L A 0.0000
221 L A 0.4270
222 E A -0.1118
223 F A 0.1524
224 V A 0.0000
225 T A -0.3906
226 A A 0.0000
227 A A 0.1274
228 G A 0.3749
229 I A 1.2246
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 -0.8384 2.4744 View CSV PDB
4.5 -0.912 2.4423 View CSV PDB
5.0 -1.0028 2.4162 View CSV PDB
5.5 -1.0939 2.3979 View CSV PDB
6.0 -1.1669 2.3738 View CSV PDB
6.5 -1.2079 2.3338 View CSV PDB
7.0 -1.2138 2.2814 View CSV PDB
7.5 -1.194 2.2237 View CSV PDB
8.0 -1.1595 2.1657 View CSV PDB
8.5 -1.1147 2.1125 View CSV PDB
9.0 -1.0594 2.0709 View CSV PDB