Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: LT56B] [mutate: IK45B] [mutate: VK3D] [mutate: TL56B] [mutate: LS56B]

Status: done

Started: 2025-04-25 14:08:01
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNASLALSASIGRVRELCAQARGAASKVKV
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 LS56B
Energy difference between WT (input) and mutated protein (by FoldX) -0.0448052 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                                                       (00:01:46)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:48)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/fffe0c9f08a5061/tmp/folded.pdb                (00:01:48)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:08)
Show buried residues
Minimal score value
-4.4285
Maximal score value
0.7187
Average score
-1.7174
Total score value
-405.3057
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 -2.7605
16 Q B -2.3271
17 D B -2.3288
18 L B -2.3811
19 G B -1.7900
20 Q B -1.7606
21 A B 0.0000
22 V B 0.0000
23 L B -0.0226
24 D B -1.1149
25 A B 0.0000
26 G B -1.0106
27 H B -1.2964
28 S B -1.4232
29 V B 0.0000
30 S B -1.3325
31 T B -1.4047
32 L B 0.0000
33 E B -2.3460
34 K B -2.3667
35 T B -1.4962
36 L B 0.0000
37 P B -1.2943
38 Q B -1.3620
39 L B 0.0000
40 L B -0.5552
41 A B -0.9697
42 K B -1.6796
43 L B 0.0000
44 S B -2.0420
45 K B -2.9683
46 L B 0.0000
47 E B -3.2585
48 N B -2.6697
49 R B -1.8685
50 G B -0.8617
51 V B 0.7187
52 H B -0.4783
53 N B -1.2444
54 A B 0.0000
55 S B -0.6182
56 S B -0.5226 mutated: LS56B
57 A B -0.5811
58 L B 0.0000
59 S B -0.4724
60 A B -0.4995
61 S B -0.9541
62 I B 0.0000
63 G B -1.8687
64 R B -2.3554
65 V B 0.0000
66 R B -2.7914
67 E B -3.2151
68 L B 0.0000
69 C B 0.0000
70 A B -1.9712
71 Q B -2.2466
72 A B 0.0000
73 R B -2.3570
74 G B -1.6706
75 A B -1.7605
76 A B -1.4639
77 S B -1.6437
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 -2.2973
3 R C -3.3122
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 -2.1561
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 -1.4070
22 S C -1.1779
23 K C -1.4499
24 L C -1.2638
25 Q C -1.6271
26 L C -1.2893
27 L C 0.0000
28 K C -2.3173
29 D C -2.5069
30 L C 0.0000
31 E C -3.5140
32 R C -4.2372
33 K C -4.0695
34 Y C 0.0000
35 E C -4.4285
36 D C -4.3433
37 N C -3.3066
38 Q C -3.0450
39 R C -3.5550
40 Y C -2.0931
41 L C 0.0000
42 E C -2.7250
43 D C -2.4920
44 K C -2.0535
45 A C -1.8214
46 Q C -2.2446
47 E C -2.3506
48 L C 0.0000
49 A C -1.8465
50 R C -2.7553
51 L C -1.9072
52 E C -2.2453
53 G C -2.2224
54 E C -2.6625
55 V C 0.0000
56 R C -2.8015
57 S C -2.2452
58 L C 0.0000
59 L C -2.5537
60 K C -3.1209
61 D C -2.8341
62 I C 0.0000
63 S C -2.1545
64 Q C -2.1077
65 K C -1.5779
66 V C 0.0000
67 A C -0.5498
68 V C -0.0522
69 Y C -0.6160
70 S C -0.8442
71 T C -0.5592
72 C C -0.8932
73 R C -2.0650
1 D D -2.4894
2 T D -2.0199
3 K D -2.8532
4 D D -2.4390
5 L D -1.9351
6 N D -3.1605
7 K D -2.8535
8 L D 0.0000
9 N D -3.1106
10 E D -3.3787
11 I D 0.0000
12 E D -2.4647
13 G D -2.3203
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 -1.0155
26 D D -1.8863
27 L D 0.0000
28 D D -3.6199
29 R D -3.8628
30 K D -3.4415
31 V D 0.0000
32 S D -3.2199
33 D D -4.3039
34 L D 0.0000
35 E D -3.6861
36 N D -4.2104
37 E D -4.3499
38 A D 0.0000
39 K D -4.4117
40 K D -3.9602
41 Q D -3.1807
42 E D -3.0896
43 A D -2.0160
44 A D -1.6988
45 I D 0.0000
46 M D -1.1304
47 D D -2.4717
48 Y D -1.8676
49 N D -2.0161
50 R D -3.3552
51 D D -3.0247
52 I D 0.0000
53 E D -3.2368
54 E D -3.3790
55 I D 0.0000
56 M D -2.1328
57 K D -2.9293
58 C D -2.4614
59 I D 0.0000
60 R D -3.4808
61 N D -3.0591
62 L D 0.0000
63 E D -3.4574
64 D D -3.5230
65 I D -2.3630
66 R D -2.6948
67 K D -2.7167
68 T D -1.2597
69 L D -0.8139
70 P D -0.3045
71 S D -0.5153
72 G D -0.4599
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 -1.8525 1.5632 View CSV PDB
4.5 -1.9705 1.3751 View CSV PDB
5.0 -2.1165 1.1793 View CSV PDB
5.5 -2.2619 1.026 View CSV PDB
6.0 -2.3763 0.9606 View CSV PDB
6.5 -2.4387 0.995 View CSV PDB
7.0 -2.4476 1.0991 View CSV PDB
7.5 -2.4183 1.2358 View CSV PDB
8.0 -2.3673 1.3843 View CSV PDB
8.5 -2.3009 1.5354 View CSV PDB
9.0 -2.2179 1.6835 View CSV PDB