Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: DK47D] [mutate: DK33D] [mutate: DK36C] [mutate: VK3B, IK45B, LS56B, VK3D] [mutate: DK20D]

Status: done

Started: 2025-05-14 15:00:15
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEKNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENKERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNASSALSASIGRVRELCAQARGAASKVKV
D: DTKDLNKLNEIEGTLNKAKDEMKVSDLDRKVSKLENEAKKQEAAIMKYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
input PDB
Selected Chain(s) B,C,D
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Mutated residues DK20D
Energy difference between WT (input) and mutated protein (by FoldX) -0.701059 kcal/mol
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 partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:03:24)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:55)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/ce3b965e6f55224/tmp/folded.pdb                (00:03:55)
[INFO]       Main:     Simulation completed successfully.                                          (00:08:12)
Show buried residues
Minimal score value
-4.6784
Maximal score value
0.7852
Average score
-1.7525
Total score value
-413.5842
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 E B -3.9528
2 N B -4.0329
3 K B -4.3143
4 E B -4.6784
5 R B -4.4233
6 W B -2.5741
7 Q B -2.9691
8 G B -3.0344
9 Q B -2.4797
10 Y B -1.6961
11 E B -3.0367
12 G B -2.1057
13 L B -1.2647
14 R B -3.1985
15 G B -3.0882
16 Q B -2.6316
17 D B -2.9376
18 L B -2.8656
19 G B -2.0343
20 Q B -1.9873
21 A B -2.0092
22 V B 0.0000
23 L B -0.0578
24 D B -1.1545
25 A B 0.0000
26 G B -1.0049
27 H B -1.2924
28 S B -1.3873
29 V B 0.0000
30 S B -1.3323
31 T B -1.4045
32 L B 0.0000
33 E B -2.3732
34 K B -2.4211
35 T B -1.5816
36 L B 0.0000
37 P B -1.4007
38 Q B -1.5877
39 L B 0.0000
40 L B -0.5864
41 A B -0.9808
42 K B -1.6870
43 L B 0.0000
44 S B -1.9540
45 K B -2.9294
46 L B 0.0000
47 E B -3.1384
48 N B -2.6181
49 R B -1.8355
50 G B -0.8008
51 V B 0.7852
52 H B -0.3465
53 N B -1.2029
54 A B 0.0000
55 S B -0.6175
56 S B -0.4992
57 A B -0.5787
58 L B 0.0000
59 S B -0.4412
60 A B -0.5055
61 S B -0.8869
62 I B 0.0000
63 G B -1.6585
64 R B -2.2103
65 V B 0.0000
66 R B -2.2161
67 E B -2.9618
68 L B 0.0000
69 C B 0.0000
70 A B -1.8347
71 Q B -2.1783
72 A B 0.0000
73 R B -2.3566
74 G B -1.6705
75 A B -1.7603
76 A B -1.4638
77 S B -1.6437
78 K B -2.2344
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.9604
2 A C -2.5756
3 R C -3.9823
4 R C -3.8155
5 K C -2.9974
6 A C 0.0000
7 E C -2.9567
8 M C -1.7693
9 L C 0.0000
10 Q C -2.1959
11 N C -2.3573
12 E C -1.9219
13 A C 0.0000
14 K C -2.2572
15 T C -1.5026
16 L C -1.0030
17 L C -1.3199
18 A C -0.9499
19 Q C -1.2554
20 A C 0.0000
21 N C -1.4332
22 S C -1.1829
23 K C -1.4858
24 L C -1.3553
25 Q C -1.7680
26 L C -1.4874
27 L C 0.0000
28 K C -2.6254
29 D C -2.9225
30 L C 0.0000
31 E C -3.7708
32 R C -4.2173
33 K C -3.6022
34 Y C 0.0000
35 E C -4.1757
36 K C -3.7290
37 N C 0.0000
38 Q C -2.8387
39 R C -3.3629
40 Y C -1.9646
41 L C 0.0000
42 E C -2.7409
43 D C -2.4519
44 K C -2.0624
45 A C -1.8710
46 Q C -2.3393
47 E C -2.3646
48 L C 0.0000
49 A C -1.8701
50 R C -2.7803
51 L C -1.9332
52 E C -2.2147
53 G C -2.2497
54 E C -2.6920
55 V C 0.0000
56 R C -2.8700
57 S C -2.2804
58 L C 0.0000
59 L C -2.5773
60 K C -3.1387
61 D C -2.8436
62 I C 0.0000
63 S C -2.1542
64 Q C -2.1075
65 K C -1.5779
66 V C 0.0000
67 A C -0.5498
68 V C -0.0522
69 Y C -0.6160
70 S C -0.8442
71 T C -0.5592
72 C C -0.8932
73 R C -2.0650
1 D D -2.4904
2 T D -2.0204
3 K D -2.8539
4 D D -2.4902
5 L D -1.9839
6 N D -3.1610
7 K D -2.8531
8 L D 0.0000
9 N D -3.1108
10 E D -3.3905
11 I D 0.0000
12 E D -2.4953
13 G D -2.3603
14 T D -2.1902
15 L D 0.0000
16 N D -2.5210
17 K D -3.3678
18 A D 0.0000
19 K D -2.5772
20 K D -3.1553 mutated: DK20D
21 E D -2.4813
22 M D -1.9151
23 K D -2.3441
24 V D -0.0283
25 S D -0.9852
26 D D -1.8653
27 L D 0.0000
28 D D -3.5853
29 R D -3.8066
30 K D -3.3318
31 V D 0.0000
32 S D -3.0572
33 K D -3.9970
34 L D 0.0000
35 E D -3.4342
36 N D -3.7427
37 E D -3.4420
38 A D 0.0000
39 K D -3.8228
40 K D -3.3865
41 Q D -2.4347
42 E D -1.9837
43 A D -1.4991
44 A D -1.4061
45 I D 0.0000
46 M D -0.9611
47 K D -2.2514
48 Y D -1.6752
49 N D -1.9263
50 R D -3.1754
51 D D -2.6148
52 I D 0.0000
53 E D -3.1713
54 E D -3.2461
55 I D 0.0000
56 M D -2.2383
57 K D -3.2423
58 C D -2.5510
59 I D 0.0000
60 R D -3.6037
61 N D -3.1591
62 L D 0.0000
63 E D -3.5004
64 D D -3.5249
65 I D -2.3644
66 R D -2.6961
67 K D -2.7177
68 T D -1.2603
69 L D -0.8139
70 P D -0.3045
71 S D -0.5153
72 G D -0.4599
73 C D -0.8806
74 H D -1.6863
75 N D -2.1327
76 T D -0.9769
77 P D -0.7362
78 S D -0.3630
79 I D 0.3722
80 E D -1.8395
81 K D -2.1345
82 P D -1.2832
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 partially or entirely disordered. Average score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -2.1352 1.5632 View CSV PDB
4.5 -2.2323 1.3751 View CSV PDB
5.0 -2.3497 1.1793 View CSV PDB
5.5 -2.4584 1.026 View CSV PDB
6.0 -2.5256 0.9606 View CSV PDB
6.5 -2.5298 0.995 View CSV PDB
7.0 -2.475 1.0991 View CSV PDB
7.5 -2.3824 1.2358 View CSV PDB
8.0 -2.2703 1.3843 View CSV PDB
8.5 -2.1462 1.5354 View CSV PDB
9.0 -2.0121 1.6835 View CSV PDB