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

Status: done

Started: 2026-02-24 21:57:00
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQAISLLQLLKDLERKYEDIQRYLEDKAQELARLEAEVRSLLKDISQKVAVYETCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNASLALSASIGRVRELCAQARGAASKVKV
D: DTVDLNKLNEIEGTLNKAKDEMKVSDLDRKVSDLENEAKKQEAAIMDYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
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 KL19D
Energy difference between WT (input) and mutated protein (by FoldX) -0.397094 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                                                       (00:03:11)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:34)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/977ab02e686dcc9/tmp/folded.pdb                (00:03:34)
[INFO]       Main:     Simulation completed successfully.                                          (00:06:17)
Show buried residues
Minimal score value
-4.4423
Maximal score value
1.287
Average score
-1.5462
Total score value
-364.9035
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 -2.3283
18 L B -2.3753
19 G B -1.3661
20 Q B -1.7578
21 A B 0.0000
22 V B 0.0000
23 L B -0.0036
24 D B -1.1148
25 A B 0.0000
26 G B -0.9979
27 H B -1.2964
28 S B -1.4761
29 V B 0.0000
30 S B -1.3324
31 T B -1.4032
32 L B 0.0000
33 E B -2.2987
34 K B -2.3828
35 T B -1.0934
36 L B 0.0000
37 P B -1.3321
38 Q B -1.1845
39 L B 0.0000
40 L B 0.0072
41 A B -0.0228
42 K B -0.3370
43 L B 0.0000
44 S B -0.2657
45 I B 0.7310
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 -0.0631
53 N B -0.6111
54 A B 0.0000
55 S B 0.2873
56 L B 1.2870
57 A B 0.2996
58 L B 0.0000
59 S B 0.1374
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 -2.8577
67 E B -3.2548
68 L B 0.0000
69 C B 0.0000
70 A B -1.9984
71 Q B -2.2803
72 A B 0.0000
73 R B -2.3640
74 G B -1.6791
75 A B -1.7686
76 A B -1.4622
77 S B -1.6463
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 -2.2924
3 R C -3.3087
4 R C -3.4356
5 K C -2.7347
6 A C 0.0000
7 E C -2.5121
8 M C -1.6747
9 L C 0.0000
10 Q C -2.2925
11 N C -2.6583
12 E C -2.3106
13 A C 0.0000
14 K C -2.4742
15 T C -1.4849
16 L C -0.7578
17 L C -0.7224
18 A C -0.1008
19 Q C -0.4069
20 A C 0.0000
21 I C 1.0398
22 S C 0.2118
23 L C -0.0596
24 L C -0.1128
25 Q C -0.7579
26 L C -0.6640
27 L C 0.0000
28 K C -2.1501
29 D C -2.3646
30 L C 0.0000
31 E C -2.8821
32 R C -4.1539
33 K C -3.9536
34 Y C 0.0000
35 E C -4.4423
36 D C -4.3449
37 I C 0.0000
38 Q C -3.2587
39 R C -3.6839
40 Y C -2.1678
41 L C 0.0000
42 E C -2.8726
43 D C -2.5615
44 K C -2.1267
45 A C -1.7056
46 Q C -2.3911
47 E C -2.4114
48 L C 0.0000
49 A C -1.7753
50 R C -2.6223
51 L C -1.7650
52 E C -2.0436
53 A C -1.7551
54 E C -2.4071
55 V C 0.0000
56 R C -2.6534
57 S C -2.1185
58 L C 0.0000
59 L C -2.4982
60 K C -3.1172
61 D C -2.8214
62 I C 0.0000
63 S C -2.1542
64 Q C -2.2820
65 K C -1.8195
66 V C 0.0000
67 A C -1.1202
68 V C -0.5790
69 Y C -1.4423
70 E C -2.5021
71 T C -1.3651
72 C C -1.3812
73 R C -2.2953
1 D D -1.3005
2 T D -0.2915
3 V D 0.6647
4 D D -0.6704
5 L D -0.7320
6 N D -1.9266
7 K D -1.8310
8 L D 0.0000
9 N D -3.0860
10 E D -3.3793
11 I D 0.0000
12 E D -2.5783
13 G D -2.3811
14 T D -2.1960
15 L D 0.0000
16 N D -2.5295
17 K D -3.3193
18 A D 0.0000
19 L D -2.2043 mutated: KL19D
20 D D -3.0417
21 E D -2.4128
22 M D -1.8058
23 K D -2.2523
24 V D 0.0065
25 S D -1.0220
26 D D -1.8899
27 L D 0.0000
28 D D -3.5288
29 R D -3.8659
30 K D -3.4465
31 V D 0.0000
32 S D -3.2020
33 D D -4.2651
34 L D 0.0000
35 E D -3.6338
36 N D -4.1223
37 E D -4.1713
38 A D 0.0000
39 K D -4.3284
40 K D -3.8638
41 Q D -3.0649
42 E D -2.9612
43 A D -1.9630
44 A D -1.6665
45 I D 0.0000
46 M D -1.1119
47 D D -2.4617
48 Y D -1.8644
49 N D -2.0249
50 R D -3.3638
51 D D -3.0369
52 I D 0.0000
53 E D -3.2484
54 E D -3.4095
55 I D 0.0000
56 M D -2.1348
57 K D -2.9220
58 C D -2.4643
59 I D 0.0000
60 R D -3.4646
61 N D -3.0402
62 L D 0.0000
63 E D -3.4091
64 D D -3.4964
65 I D -2.3349
66 R D -2.6460
67 K D -2.6907
68 T D -1.2441
69 L D -0.8033
70 P D -0.3006
71 S D -0.5165
72 G D -0.6411
73 C D -1.1876
74 H D -1.9546
75 N D -2.4497
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 -1.5546 1.7894 View CSV PDB
4.5 -1.6742 1.7898 View CSV PDB
5.0 -1.8257 1.791 View CSV PDB
5.5 -1.9811 1.7939 View CSV PDB
6.0 -2.1104 1.7991 View CSV PDB
6.5 -2.1917 1.8051 View CSV PDB
7.0 -2.221 1.8095 View CSV PDB
7.5 -2.2118 1.8117 View CSV PDB
8.0 -2.1803 1.8126 View CSV PDB
8.5 -2.1335 1.8129 View CSV PDB
9.0 -2.0699 1.813 View CSV PDB