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

Status: done

Started: 2026-02-24 22:04:17
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQAISLLQLLKDLERKYEDIQRYLEDKAQELARLEAEVRSLLKDISQKVAVYETCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNASLALSASIGRVRELCAQARGAASKVKV
D: DTVDLNKLNEIEGTLNKALDEMKVSDLDRKVSDLENEAKKQEAAIMDYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
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 EL35D
Energy difference between WT (input) and mutated protein (by FoldX) -1.56879 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                                                       (00:02:57)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:03)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/25cb78bfb59f0f1/tmp/folded.pdb                (00:03:03)
[INFO]       Main:     Simulation completed successfully.                                          (00:05:31)
Show buried residues
Minimal score value
-4.4337
Maximal score value
1.2872
Average score
-1.5209
Total score value
-358.9246
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 -2.7574
16 Q B -2.3268
17 D B -2.3276
18 L B -2.3750
19 G B -1.3652
20 Q B -1.7554
21 A B 0.0000
22 V B 0.0000
23 L B 0.0022
24 D B -1.1122
25 A B 0.0000
26 G B -0.9960
27 H B -1.2943
28 S B -1.4768
29 V B 0.0000
30 S B -1.3321
31 T B -1.4031
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 0.2863
56 L B 1.2872
57 A B 0.2990
58 L B 0.0000
59 S B 0.1375
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 -2.8591
67 E B -3.2575
68 L B 0.0000
69 C B 0.0000
70 A B -2.0026
71 Q B -2.2901
72 A B 0.0000
73 R B -2.3664
74 G B -1.6821
75 A B -1.7703
76 A B -1.4629
77 S B -1.6474
78 K B -2.4655
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.8245
2 A C -2.2949
3 R C -3.3124
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 -2.3033
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 -3.9262
34 Y C 0.0000
35 E C -4.4337
36 D C -4.3361
37 I C 0.0000
38 Q C -3.2569
39 R C -3.6840
40 Y C -2.1720
41 L C 0.0000
42 E C -2.8784
43 D C -2.5649
44 K C -2.1293
45 A C -1.7077
46 Q C -2.3926
47 E C -2.4121
48 L C 0.0000
49 A C -1.7753
50 R C -2.6223
51 L C -1.7664
52 E C -2.0460
53 A C -1.7578
54 E C -2.4100
55 V C 0.0000
56 R C -2.6616
57 S C -2.1226
58 L C 0.0000
59 L C -2.4984
60 K C -3.1172
61 D C -2.8216
62 I C 0.0000
63 S C -2.1539
64 Q C -2.2811
65 K C -1.8193
66 V C 0.0000
67 A C -1.1196
68 V C -0.5785
69 Y C -1.4418
70 E C -2.5013
71 T C -1.3637
72 C C -1.3805
73 R C -2.2950
1 D D -1.3005
2 T D -0.2926
3 V D 0.6626
4 D D -0.6725
5 L D -0.7347
6 N D -1.9306
7 K D -1.8383
8 L D 0.0000
9 N D -3.0887
10 E D -3.3821
11 I D 0.0000
12 E D -2.5811
13 G D -2.3824
14 T D -2.1964
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 -2.5192
33 D D -3.6477
34 L D 0.0000
35 L D -1.7651 mutated: EL35D
36 N D -3.2029
37 E D -3.5519
38 A D 0.0000
39 K D -3.8624
40 K D -3.6100
41 Q D -2.8751
42 E D -2.9642
43 A D -1.9727
44 A D -1.6782
45 I D 0.0000
46 M D -1.1427
47 D D -2.4816
48 Y D -1.8811
49 N D -2.0484
50 R D -3.3867
51 D D -3.0551
52 I D 0.0000
53 E D -3.2898
54 E D -3.4298
55 I D 0.0000
56 M D -2.1491
57 K D -2.9323
58 C D -2.4704
59 I D 0.0000
60 R D -3.4660
61 N D -3.0415
62 L D 0.0000
63 E D -3.4125
64 D D -3.4984
65 I D -2.3361
66 R D -2.6467
67 K D -2.6917
68 T D -1.2446
69 L D -0.8033
70 P D -0.3006
71 S D -0.5165
72 G D -0.6411
73 C D -1.1873
74 H D -1.9544
75 N D -2.4494
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 -1.5362 1.79 View CSV PDB
4.5 -1.6538 1.7904 View CSV PDB
5.0 -1.8023 1.7915 View CSV PDB
5.5 -1.9543 1.7943 View CSV PDB
6.0 -2.0804 1.7993 View CSV PDB
6.5 -2.1592 1.8054 View CSV PDB
7.0 -2.1868 1.81 View CSV PDB
7.5 -2.1766 1.8123 View CSV PDB
8.0 -2.1447 1.8132 View CSV PDB
8.5 -2.0977 1.8135 View CSV PDB
9.0 -2.034 1.8136 View CSV PDB