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

Status: done

Started: 2025-05-14 14:48:30
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEKNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNASLALSASIGRVRELCAQARGAASKVKV
D: DTVDLNKLNEIEGTLNKAKDEMKVSDLDRKVSKLENEAKKQEAAIMKYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
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 IK45B,LS56B,VK3D,VK3B
Energy difference between WT (input) and mutated protein (by FoldX) -1.40568 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                                                       (00:02:10)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:04)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/4d8f321580d315e/tmp/folded.pdb                (00:03:04)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:25)
Show buried residues
Minimal score value
-4.6784
Maximal score value
0.7848
Average score
-1.7499
Total score value
-412.972
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 mutated: VK3B
4 E B -4.6784
5 R B -4.4233
6 W B -2.5741
7 Q B -2.9691
8 G B -3.0295
9 Q B -2.4730
10 Y B -1.6836
11 E B -3.0188
12 G B -2.0886
13 L B -1.2378
14 R B -3.1451
15 G B -3.0586
16 Q B -2.6090
17 D B -2.9062
18 L B -2.8426
19 G B -2.0234
20 Q B -1.9798
21 A B -2.0044
22 V B 0.0000
23 L B -0.0655
24 D B -1.1606
25 A B 0.0000
26 G B -1.0102
27 H B -1.2959
28 S B -1.3894
29 V B 0.0000
30 S B -1.3329
31 T B -1.4047
32 L B 0.0000
33 E B -2.3554
34 K B -2.3840
35 T B -1.5234
36 L B 0.0000
37 P B -1.3430
38 Q B -1.4568
39 L B 0.0000
40 L B -0.5885
41 A B -1.0039
42 K B -1.7987
43 L B 0.0000
44 S B -1.9916
45 K B -2.9879 mutated: IK45B
46 L B 0.0000
47 E B -3.1630
48 N B -2.6192
49 R B -1.8380
50 G B -0.8017
51 V B 0.7848
52 H B -0.3469
53 N B -1.2029
54 A B 0.0000
55 S B -0.6174
56 S B -0.4992 mutated: LS56B
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 -2.2094
67 E B -2.9491
68 L B 0.0000
69 C B 0.0000
70 A B -1.8118
71 Q B -2.1311
72 A B 0.0000
73 R B -2.3413
74 G B -1.6533
75 A B -1.7477
76 A B -1.4572
77 S B -1.6388
78 K B -2.2342
79 V B 0.0000
80 K B -1.2777
81 V B 0.6642
1 D C -2.9580
2 A C -2.5690
3 R C -3.9627
4 R C -3.8077
5 K C -2.9903
6 A C 0.0000
7 E C -2.9453
8 M C -1.7602
9 L C 0.0000
10 Q C -2.1936
11 N C -2.3541
12 E C -1.9196
13 A C 0.0000
14 K C -2.2568
15 T C -1.5026
16 L C -1.0030
17 L C -1.3199
18 A C -0.9503
19 Q C -1.2560
20 A C 0.0000
21 N C -1.4148
22 S C -1.1774
23 K C -1.4955
24 L C -1.3424
25 Q C -1.7636
26 L C -1.4667
27 L C 0.0000
28 K C -2.5914
29 D C -2.8937
30 L C 0.0000
31 E C -3.7762
32 R C -4.2025
33 K C -3.6005
34 Y C 0.0000
35 E C -4.1704
36 K C -3.7129
37 N C 0.0000
38 Q C -2.8328
39 R C -3.3560
40 Y C -1.9569
41 L C 0.0000
42 E C -2.7382
43 D C -2.4511
44 K C -2.0618
45 A C -1.8707
46 Q C -2.3391
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 -2.2500
54 E C -2.6923
55 V C 0.0000
56 R C -2.8659
57 S C -2.2811
58 L C 0.0000
59 L C -2.5699
60 K C -3.1398
61 D C -2.8443
62 I C 0.0000
63 S C -2.1491
64 Q C -2.1077
65 K C -1.5782
66 V C 0.0000
67 A C -0.5495
68 V C -0.0529
69 Y C -0.6170
70 S C -0.8440
71 T C -0.5591
72 C C -0.8940
73 R C -2.0653
1 D D -2.4887
2 T D -2.0190
3 K D -2.8529 mutated: VK3D
4 D D -2.4879
5 L D -1.9792
6 N D -3.1606
7 K D -2.8568
8 L D 0.0000
9 N D -3.1110
10 E D -3.3798
11 I D 0.0000
12 E D -2.4644
13 G D -2.3208
14 T D -2.1617
15 L D 0.0000
16 N D -2.4327
17 K D -3.3492
18 A D 0.0000
19 K D -2.5868
20 D D -3.2259
21 E D -2.5333
22 M D -1.9449
23 K D -2.3844
24 V D -0.0608
25 S D -1.0056
26 D D -1.8686
27 L D 0.0000
28 D D -3.5854
29 R D -3.8067
30 K D -3.3319
31 V D 0.0000
32 S D -3.0509
33 K D -3.9854
34 L D 0.0000
35 E D -3.4201
36 N D -3.7241
37 E D -3.4022
38 A D 0.0000
39 K D -3.8173
40 K D -3.3811
41 Q D -2.4387
42 E D -2.0092
43 A D -1.5140
44 A D -1.4210
45 I D 0.0000
46 M D -0.9876
47 K D -2.2647
48 Y D -1.6843
49 N D -1.9334
50 R D -3.1805
51 D D -2.6176
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 -3.5007
64 D D -3.5249
65 I D -2.3644
66 R D -2.6965
67 K D -2.7178
68 T D -1.2605
69 L D -0.8146
70 P D -0.3064
71 S D -0.5173
72 G D -0.4635
73 C D -0.8835
74 H D -1.6878
75 N D -2.1334
76 T D -0.9772
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
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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 -2.077 1.5632 View CSV PDB
4.5 -2.1809 1.3751 View CSV PDB
5.0 -2.3063 1.1793 View CSV PDB
5.5 -2.425 1.026 View CSV PDB
6.0 -2.5054 0.9606 View CSV PDB
6.5 -2.525 0.995 View CSV PDB
7.0 -2.4859 1.0991 View CSV PDB
7.5 -2.4081 1.2358 View CSV PDB
8.0 -2.3101 1.3843 View CSV PDB
8.5 -2.1989 1.5354 View CSV PDB
9.0 -2.0755 1.6835 View CSV PDB