Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: LT56B] [mutate: IK45B] [mutate: VK3D] [mutate: TL56B] [mutate: LS56B] [mutate: SL56B, NA53B] [mutate: AN53B] [mutate: SK55B] [mutate: KR55B] [mutate: RH55B] [mutate: KI45B, HT55B]

Status: done

Started: 2025-04-25 14:40:31
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNAHLALSASIGRVRELCAQARGAASKVKV
D: DTKDLNKLNEIEGTLNKAKDEMKVSDLDRKVSDLENEAKKQEAAIMDYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
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 KI45B,HT55B
Energy difference between WT (input) and mutated protein (by FoldX) -2.73901 kcal/mol
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[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                                                       (00:02:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:38)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/5c2173af1d33325/tmp/folded.pdb                (00:02:38)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:48)
Show buried residues
Minimal score value
-4.4392
Maximal score value
1.2937
Average score
-1.6487
Total score value
-389.0891
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 -1.0148
14 R B -2.7222
15 G B -2.7609
16 Q B -2.3271
17 D B -2.3268
18 L B -2.3788
19 G B -1.7850
20 Q B -1.7536
21 A B 0.0000
22 V B 0.0000
23 L B -0.0015
24 D B -1.1042
25 A B 0.0000
26 G B -0.9998
27 H B -1.2898
28 S B -1.4196
29 V B 0.0000
30 S B -1.3317
31 T B -1.4042
32 L B 0.0000
33 E B -2.3480
34 K B -2.3704
35 T B -1.5021
36 L B 0.0000
37 P B -1.3003
38 Q B -1.3768
39 L B 0.0000
40 L B -0.0430
41 A B -0.0063
42 K B -0.4020
43 L B 0.0000
44 S B -0.2439
45 I B 0.7677 mutated: KI45B
46 L B 0.0000
47 E B -2.0864
48 N B -1.4529
49 R B -0.8389
50 G B -0.4029
51 V B 1.0297
52 H B -0.0976
53 N B -0.6790
54 A B 0.0000
55 T B 0.2125 mutated: HT55B
56 L B 1.2937
57 A B 0.2070
58 L B 0.0000
59 S B 0.1468
60 A B -0.0345
61 S B -0.7097
62 I B 0.0000
63 G B -1.8935
64 R B -2.3881
65 V B 0.0000
66 R B -2.8700
67 E B -3.2650
68 L B 0.0000
69 C B 0.0000
70 A B -2.0122
71 Q B -2.3067
72 A B 0.0000
73 R B -2.3711
74 G B -1.6876
75 A B -1.7731
76 A B -1.4650
77 S B -1.6490
78 K B -2.2344
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.8246
2 A C -2.2978
3 R C -3.3125
4 R C -3.4357
5 K C -2.7288
6 A C 0.0000
7 E C -2.4558
8 M C -1.5637
9 L C 0.0000
10 Q C -2.1533
11 N C -2.4593
12 E C -1.9674
13 A C 0.0000
14 K C -2.3355
15 T C -1.5608
16 L C -1.0340
17 L C -1.3431
18 A C -0.9505
19 Q C -1.2562
20 A C 0.0000
21 N C -1.4090
22 S C -1.1774
23 K C -1.4508
24 L C -1.2669
25 Q C -1.6138
26 L C -1.2717
27 L C 0.0000
28 K C -2.2695
29 D C -2.4762
30 L C 0.0000
31 E C -2.8920
32 R C -4.1806
33 K C -4.0483
34 Y C 0.0000
35 E C -4.4115
36 D C -4.4392
37 N C -3.4285
38 Q C -3.2572
39 R C -3.8867
40 Y C -2.4082
41 L C 0.0000
42 E C -3.6256
43 D C -2.9480
44 K C -2.3611
45 A C -1.9781
46 Q C -2.5603
47 E C -2.5083
48 L C 0.0000
49 A C -1.8773
50 R C -2.7779
51 L C -1.9238
52 E C -2.2742
53 G C -2.2312
54 E C -2.6667
55 V C 0.0000
56 R C -2.8311
57 S C -2.2496
58 L C 0.0000
59 L C -2.5516
60 K C -3.1199
61 D C -2.8202
62 I C 0.0000
63 S C -2.1533
64 Q C -2.1087
65 K C -1.5807
66 V C 0.0000
67 A C -0.5524
68 V C -0.0556
69 Y C -0.6186
70 S C -0.8456
71 T C -0.5602
72 C C -0.8932
73 R C -2.0650
1 D D -2.4902
2 T D -2.0202
3 K D -2.8534
4 D D -2.4378
5 L D -1.9349
6 N D -3.1591
7 K D -2.8468
8 L D 0.0000
9 N D -3.1094
10 E D -3.3769
11 I D 0.0000
12 E D -2.4636
13 G D -2.3198
14 T D -2.1613
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 -1.0155
26 D D -1.8863
27 L D 0.0000
28 D D -3.6199
29 R D -3.8628
30 K D -3.4405
31 V D 0.0000
32 S D -3.1808
33 D D -4.2328
34 L D 0.0000
35 E D -3.5940
36 N D -4.0713
37 E D -4.0854
38 A D 0.0000
39 K D -4.3197
40 K D -3.8542
41 Q D -3.0786
42 E D -3.0717
43 A D -1.9996
44 A D -1.6971
45 I D 0.0000
46 M D -1.1512
47 D D -2.4846
48 Y D -1.8878
49 N D -2.0358
50 R D -3.3699
51 D D -3.0388
52 I D 0.0000
53 E D -3.2510
54 E D -3.4166
55 I D 0.0000
56 M D -2.1358
57 K D -2.9237
58 C D -2.4676
59 I D 0.0000
60 R D -3.4665
61 N D -3.0412
62 L D 0.0000
63 E D -3.4158
64 D D -3.4983
65 I D -2.3361
66 R D -2.6465
67 K D -2.6917
68 T D -1.2446
69 L D -0.8039
70 P D -0.3015
71 S D -0.5175
72 G D -0.4612
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
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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 -1.7148 1.8656 View CSV PDB
4.5 -1.8348 1.8664 View CSV PDB
5.0 -1.9839 1.8686 View CSV PDB
5.5 -2.1333 1.8732 View CSV PDB
6.0 -2.253 1.8799 View CSV PDB
6.5 -2.3218 1.8861 View CSV PDB
7.0 -2.3375 1.8897 View CSV PDB
7.5 -2.315 1.8912 View CSV PDB
8.0 -2.2708 1.8918 View CSV PDB
8.5 -2.211 1.8919 View CSV PDB
9.0 -2.1346 1.892 View CSV PDB