Project name: sod

Status: done

Started: 2025-06-27 05:55:46
Chain sequence(s) C: ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
B: ATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ
input PDB
Selected Chain(s) C,B
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                                          (00:08:11)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/21580a1f91c6563/tmp/folded.pdb                (00:08:11)
[INFO]       Main:     Simulation completed successfully.                                          (00:12:24)
Show buried residues
Minimal score value
-3.8694
Maximal score value
1.8555
Average score
-0.8942
Total score value
-273.6203
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 A B -1.6272
2 T B -1.1899
3 K B -1.1144
4 A B 0.0000
5 V B 1.1188
6 C B 0.0000
7 V B 1.1649
8 L B 0.0000
9 K B -1.9391
10 G B -2.0918
11 D B -2.8700
12 G B -2.3513
13 P B -1.7670
14 V B 0.0000
15 Q B -1.4022
16 G B 0.0000
17 I B 1.2156
18 I B 0.0000
19 N B -0.1756
20 F B 0.0000
21 E B -2.5756
22 Q B 0.0000
23 K B -3.3438
24 E B -3.2610
25 S B -2.2172
26 N B -2.4170
27 G B -2.1656
28 P B -2.0481
29 V B 0.0000
30 K B -2.8588
31 V B 0.0000
32 W B -0.7012
33 G B 0.0120
34 S B -0.8577
35 I B 0.0000
36 K B -2.2903
37 G B -1.5303
38 L B 0.0000
39 T B -2.3916
40 E B -3.0005
41 G B -1.2790
42 L B -0.1364
43 H B 0.0000
44 G B 0.0000
45 F B 0.0000
46 H B 0.0000
47 V B 0.0000
48 H B 0.0000
49 E B -0.0496
50 F B 0.7515
51 G B -0.2005
52 D B -1.0904
53 N B -1.5043
54 T B -1.0622
55 A B -0.7357
56 G B -1.5960
57 C B -0.9981
58 T B -0.6878
59 S B -0.5667
60 A B 0.0000
61 G B -0.1771
62 P B -0.4457
63 H B 0.0000
64 F B 0.0000
65 N B -0.6323
66 P B -0.2579
67 L B 0.3159
68 S B -0.6776
69 R B -2.3015
70 K B -2.7940
71 H B 0.0000
72 G B 0.0000
73 G B 0.0000
74 P B -1.6776
75 K B -2.6780
76 D B -2.9779
77 E B -3.0920
78 E B -2.7925
79 R B 0.0000
80 H B 0.0000
81 V B 0.0000
82 G B 0.0000
83 D B 0.0000
84 L B 0.0000
85 G B 0.0000
86 N B -0.0827
87 V B 0.0000
88 T B -0.8817
89 A B 0.0000
90 D B -3.3642
91 K B -3.6717
92 D B -3.5386
93 G B 0.0000
94 V B -2.6009
95 A B 0.0000
96 D B -2.1859
97 V B 0.0000
98 S B -1.0926
99 I B -1.0668
100 E B -2.3979
101 D B 0.0000
102 S B -1.0511
103 V B -0.4182
104 I B 0.0000
105 S B 0.0000
106 L B 0.0000
107 S B -1.2094
108 G B -1.6792
109 D B -2.0922
110 H B -1.0774
111 C B -0.8525
112 I B 0.0000
113 I B 0.5964
114 G B 0.2676
115 R B -0.0175
116 T B 0.0000
117 L B 0.0000
118 V B 0.0000
119 V B 0.0000
120 H B 0.0000
121 E B -1.9104
122 K B -1.7708
123 A B -0.6486
124 D B 0.0000
125 D B -1.0793
126 L B -1.1298
127 G B -2.4325
128 K B -2.2740
129 G B -2.2468
130 G B -2.1507
131 N B -2.8825
132 E B -3.2576
133 E B -2.8970
134 S B 0.0000
135 T B -3.0674
136 K B -3.1765
137 T B -1.7423
138 G B 0.0000
139 N B -1.9306
140 A B 0.0000
141 G B -1.3785
142 S B -1.1496
143 R B -1.1673
144 L B -1.3932
145 A B 0.0000
146 C B 0.0000
147 G B -0.1459
148 V B 0.9158
149 I B 0.0000
150 G B 1.0560
151 I B 1.7899
152 A B 0.1571
153 Q B -0.8516
1 A C -1.5917
2 T C -1.1132
3 K C -0.8353
4 A C 0.0000
5 V C 1.1834
6 C C 0.0000
7 V C 1.2780
8 L C 0.0000
9 K C -2.2570
10 G C -2.4543
11 D C -2.6333
12 G C -1.7840
13 P C -2.1283
14 V C 0.0000
15 Q C -2.1058
16 G C 0.0000
17 I C 1.1202
18 I C 0.0000
19 N C 0.0906
20 F C 0.0000
21 E C -2.5833
22 Q C 0.0000
23 K C -3.3116
24 E C -3.2720
25 S C -2.2175
26 N C -2.4271
27 G C -2.0866
28 P C -1.9677
29 V C 0.0000
30 K C -2.4720
31 V C 0.0000
32 W C -0.7225
33 G C -0.1689
34 S C -1.0468
35 I C 0.0000
36 K C -2.8042
37 G C 0.0000
38 L C 0.0000
39 T C -1.6473
40 E C -1.8066
41 G C -0.7155
42 L C 0.1592
43 H C 0.0000
44 G C 0.0000
45 F C 0.0000
46 H C 0.0000
47 V C 0.0000
48 H C 0.0000
49 E C -0.1231
50 F C 0.6611
51 G C -0.1220
52 D C -0.8113
53 N C -0.9232
54 T C -0.7430
55 A C -0.5096
56 G C -1.2818
57 C C -0.7985
58 T C -0.3987
59 S C -0.4229
60 A C 0.0000
61 G C -0.1750
62 P C -0.4647
63 H C 0.0000
64 F C 0.0000
65 N C -0.6283
66 P C -0.3711
67 L C -0.1412
68 S C -0.7226
69 R C -2.1472
70 K C -3.0754
71 H C 0.0000
72 G C 0.0000
73 G C 0.0000
74 P C -1.8399
75 K C -2.8576
76 D C -3.4154
77 E C -3.8329
78 E C -3.8694
79 R C 0.0000
80 H C 0.0000
81 V C 0.0000
82 G C 0.0000
83 D C 0.0000
84 L C 0.0000
85 G C 0.0000
86 N C -0.0907
87 V C 0.0000
88 T C -0.7639
89 A C 0.0000
90 D C -3.3797
91 K C -3.4802
92 D C -3.6583
93 G C 0.0000
94 V C 0.0000
95 A C 0.0000
96 D C -2.2719
97 V C 0.0000
98 S C -1.0566
99 I C -1.1438
100 E C -2.2693
101 D C 0.0000
102 S C -1.0176
103 V C -0.4897
104 I C 0.0000
105 S C 0.0000
106 L C 0.0000
107 S C -1.1412
108 G C -1.6664
109 D C -2.1701
110 H C -1.1552
111 C C -0.7955
112 I C 0.0000
113 I C 0.6629
114 G C 0.2636
115 R C -0.0962
116 T C 0.0000
117 L C 0.0000
118 V C 0.0000
119 V C 0.0000
120 H C 0.0000
121 E C -1.5138
122 K C -1.5016
123 A C -0.5703
124 D C 0.0000
125 D C -1.2710
126 L C -1.2143
127 G C -2.7187
128 K C -2.3387
129 G C -2.3681
130 G C -2.2411
131 N C -3.0623
132 E C -3.4307
133 E C -3.2200
134 S C 0.0000
135 T C -3.3288
136 K C -3.2265
137 T C -1.9151
138 G C 0.0000
139 N C -2.1939
140 A C 0.0000
141 G C -1.4127
142 S C -1.0904
143 R C -1.1107
144 L C -1.3435
145 A C 0.0000
146 C C 0.0000
147 G C 0.0000
148 V C 1.1124
149 I C 0.0000
150 G C 1.2701
151 I C 1.8555
152 A C 0.2327
153 Q C -0.7643
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 -0.6452 3.2554 View CSV PDB
4.5 -0.7206 3.1742 View CSV PDB
5.0 -0.8135 3.0801 View CSV PDB
5.5 -0.9081 2.9771 View CSV PDB
6.0 -0.985 2.9282 View CSV PDB
6.5 -1.0266 2.9372 View CSV PDB
7.0 -1.0281 2.9513 View CSV PDB
7.5 -1.0003 2.9685 View CSV PDB
8.0 -0.9552 2.9871 View CSV PDB
8.5 -0.8982 3.0062 View CSV PDB
9.0 -0.8303 3.0253 View CSV PDB