Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: NI21C] [mutate: KL23C] [mutate: NI37C] [mutate: GA53C] [mutate: SE70C] [mutate: KL19D] [mutate: EL35D] [mutate: NL49D, NE61D]

Status: done

Started: 2026-02-24 23:29:41
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQAISLLQLLKDLERKYEDIQRYLEDKAQELARLEAEVRSLLKDISQKVAVYETCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNASLALSASIGRVRELCAQARGAASKVKV
D: DTVDLNKLNEIEGTLNKALDEMKVSDLDRKVSDLLNEAKKQEAAIMDYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
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 NL49D,NE61D
Energy difference between WT (input) and mutated protein (by FoldX) -0.724899 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.                                                (00:00:02)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:02)
[INFO]       FoldX:    Building mutant model                                                       (00:03:00)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:04:03)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/f9256d8aa0d1057/tmp/folded.pdb                (00:04:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:37)
Show buried residues
Minimal score value
-4.4326
Maximal score value
1.2872
Average score
-1.5226
Total score value
-359.3433
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 -2.8742
2 N B -2.3304
3 V B -0.8251
4 E B -2.9698
5 R B -3.2786
6 W B -1.2831
7 Q B -1.9276
8 G B -2.4674
9 Q B -2.0528
10 Y B -1.6049
11 E B -2.8831
12 G B -1.9511
13 L B -1.0146
14 R B -2.7220
15 G B -2.7575
16 Q B -2.3268
17 D B -2.3270
18 L B -2.3742
19 G B -1.3634
20 Q B -1.7531
21 A B 0.0000
22 V B 0.0000
23 L B 0.0095
24 D B -1.1087
25 A B 0.0000
26 G B -0.9921
27 H B -1.2922
28 S B -1.4756
29 V B 0.0000
30 S B -1.3319
31 T B -1.4030
32 L B 0.0000
33 E B -2.2991
34 K B -2.3828
35 T B -1.0936
36 L B 0.0000
37 P B -1.3326
38 Q B -1.1849
39 L B 0.0000
40 L B 0.0059
41 A B -0.0234
42 K B -0.3374
43 L B 0.0000
44 S B -0.2661
45 I B 0.7308
46 L B 0.0000
47 E B -2.1291
48 N B -1.5245
49 R B -0.9834
50 G B -0.4664
51 V B 0.9702
52 H B -0.0637
53 N B -0.6116
54 A B 0.0000
55 S B 0.2862
56 L B 1.2872
57 A B 0.2990
58 L B 0.0000
59 S B 0.1368
60 A B -0.0414
61 S B -0.7151
62 I B 0.0000
63 G B -1.8954
64 R B -2.3916
65 V B 0.0000
66 R B -2.8688
67 E B -3.2203
68 L B 0.0000
69 C B 0.0000
70 A B -1.8787
71 Q B -2.1780
72 A B 0.0000
73 R B -2.0449
74 G B -1.4977
75 A B -1.6497
76 A B -1.3228
77 S B -1.5432
78 K B -2.4180
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.8245
2 A C -2.2951
3 R C -3.3126
4 R C -3.4419
5 K C -2.7422
6 A C 0.0000
7 E C -2.5277
8 M C -1.6974
9 L C 0.0000
10 Q C -2.3024
11 N C -2.6724
12 E C -2.3299
13 A C 0.0000
14 K C -2.4808
15 T C -1.4909
16 L C -0.7626
17 L C -0.7248
18 A C -0.1013
19 Q C -0.4072
20 A C 0.0000
21 I C 1.0422
22 S C 0.2163
23 L C -0.0537
24 L C -0.1077
25 Q C -0.7501
26 L C -0.4051
27 L C 0.0000
28 K C -2.1420
29 D C -2.3544
30 L C 0.0000
31 E C -2.8714
32 R C -4.1393
33 K C -3.9268
34 Y C 0.0000
35 E C -4.4326
36 D C -4.3341
37 I C 0.0000
38 Q C -3.2518
39 R C -3.6758
40 Y C -2.1582
41 L C 0.0000
42 E C -2.8674
43 D C -2.5453
44 K C -2.0623
45 A C -1.7008
46 Q C -2.3857
47 E C -2.4074
48 L C 0.0000
49 A C -1.7734
50 R C -2.6221
51 L C -1.7664
52 E C -2.0460
53 A C -1.7577
54 E C -2.4098
55 V C 0.0000
56 R C -2.6628
57 S C -2.1222
58 L C 0.0000
59 L C -2.4406
60 K C -3.1167
61 D C -2.8212
62 I C 0.0000
63 S C -2.1140
64 Q C -2.2808
65 K C -1.8191
66 V C 0.0000
67 A C -1.1191
68 V C -0.5781
69 Y C -1.4415
70 E C -2.5008
71 T C -1.3629
72 C C -1.3801
73 R C -2.2948
1 D D -1.3009
2 T D -0.2925
3 V D 0.6630
4 D D -0.6715
5 L D -0.7340
6 N D -1.9290
7 K D -1.8336
8 L D 0.0000
9 N D -3.0875
10 E D -3.3807
11 I D 0.0000
12 E D -2.5804
13 G D -2.3819
14 T D -2.1963
15 L D 0.0000
16 N D -2.5310
17 K D -3.3206
18 A D 0.0000
19 L D -2.2099
20 D D -3.0438
21 E D -2.4144
22 M D -1.8074
23 K D -2.2534
24 V D 0.0059
25 S D -1.0222
26 D D -1.8899
27 L D 0.0000
28 D D -3.5245
29 R D -3.6677
30 K D -3.1810
31 V D 0.0000
32 S D -2.5202
33 D D -3.6497
34 L D 0.0000
35 L D -1.7674
36 N D -3.2070
37 E D -3.5600
38 A D 0.0000
39 K D -3.8668
40 K D -3.6205
41 Q D -2.8878
42 E D -2.9876
43 A D -1.9615
44 A D -1.6490
45 I D 0.0000
46 M D -1.0795
47 D D -2.3953
48 Y D -1.7242
49 L D -1.7107 mutated: NL49D
50 R D -3.2342
51 D D -2.9946
52 I D 0.0000
53 E D -3.3159
54 E D -3.5465
55 I D 0.0000
56 M D -2.4346
57 K D -3.4913
58 C D -2.8430
59 I D 0.0000
60 R D -3.8607
61 E D -3.6018 mutated: NE61D
62 L D 0.0000
63 E D -3.6105
64 D D -3.6557
65 I D -2.3678
66 R D -2.6970
67 K D -2.6785
68 T D -1.2308
69 L D -0.7928
70 P D -0.3006
71 S D -0.5165
72 G D -0.6411
73 C D -1.1872
74 H D -1.9543
75 N D -2.4493
76 T D -0.9799
77 P D -0.7379
78 S D -0.3640
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 -1.5325 1.79 View CSV PDB
4.5 -1.6534 1.7904 View CSV PDB
5.0 -1.8055 1.7915 View CSV PDB
5.5 -1.9606 1.7944 View CSV PDB
6.0 -2.0881 1.7995 View CSV PDB
6.5 -2.1668 1.8055 View CSV PDB
7.0 -2.1936 1.8101 View CSV PDB
7.5 -2.1822 1.8123 View CSV PDB
8.0 -2.149 1.8132 View CSV PDB
8.5 -2.1007 1.8135 View CSV PDB
9.0 -2.036 1.8136 View CSV PDB