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

Status: done

Started: 2025-04-24 22:40:11
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNASTALSASIGRVRELCAQARGAASKVKV
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 VK3D
Energy difference between WT (input) and mutated protein (by FoldX) -0.730228 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.                                                (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:01:57)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:22)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/98c3da85a2f3e0d/tmp/folded.pdb                (00:02:22)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:38)
Show buried residues
Minimal score value
-4.4557
Maximal score value
0.7421
Average score
-1.7168
Total score value
-405.154
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 -2.4691
9 Q B -2.0551
10 Y B -1.6093
11 E B -2.8894
12 G B -1.9570
13 L B -1.0239
14 R B -2.7401
15 G B -2.7700
16 Q B -2.3344
17 D B -2.3413
18 L B -2.3923
19 G B -1.8015
20 Q B -1.7769
21 A B 0.0000
22 V B 0.0000
23 L B -0.0559
24 D B -1.1439
25 A B 0.0000
26 G B -1.0241
27 H B -1.3083
28 S B -1.4302
29 V B 0.0000
30 S B -1.3341
31 T B -1.4046
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 -1.2961
38 Q B -1.3653
39 L B 0.0000
40 L B -0.5593
41 A B -0.9760
42 K B -1.7053
43 L B 0.0000
44 S B -2.0458
45 K B -2.9826
46 L B 0.0000
47 E B -3.2587
48 N B -2.6669
49 R B -1.8703
50 G B -0.8555
51 V B 0.7421
52 H B -0.4417
53 N B -1.1894
54 A B 0.0000
55 S B -0.5360
56 T B -0.3762
57 A B -0.5065
58 L B 0.0000
59 S B -0.4223
60 A B -0.4619
61 S B -0.9333
62 I B 0.0000
63 G B -1.8687
64 R B -2.3554
65 V B 0.0000
66 R B -2.7847
67 E B -3.2025
68 L B 0.0000
69 C B 0.0000
70 A B -1.9482
71 Q B -2.1995
72 A B 0.0000
73 R B -2.3416
74 G B -1.6527
75 A B -1.7482
76 A B -1.4577
77 S B -1.6384
78 K B -2.2341
79 V B 0.0000
80 K B -1.2777
81 V B 0.6642
1 D C -2.8245
2 A C -2.2974
3 R C -3.3163
4 R C -3.4385
5 K C -2.7313
6 A C 0.0000
7 E C -2.4653
8 M C -1.5701
9 L C 0.0000
10 Q C -2.1643
11 N C -2.4630
12 E C -1.9688
13 A C 0.0000
14 K C -2.3355
15 T C -1.5606
16 L C -1.0338
17 L C -1.3430
18 A C -0.9505
19 Q C -1.2562
20 A C 0.0000
21 N C -1.4070
22 S C -1.1783
23 K C -1.4533
24 L C -1.2693
25 Q C -1.6427
26 L C -1.3085
27 L C 0.0000
28 K C -2.3621
29 D C -2.5521
30 L C 0.0000
31 E C -3.6095
32 R C -4.2873
33 K C -4.1033
34 Y C 0.0000
35 E C -4.4557
36 D C -4.3560
37 N C -3.3154
38 Q C -3.0442
39 R C -3.5514
40 Y C -2.0882
41 L C 0.0000
42 E C -2.7023
43 D C -2.4812
44 K C -2.0454
45 A C -1.7954
46 Q C -2.2355
47 E C -2.3457
48 L C 0.0000
49 A C -1.8451
50 R C -2.7543
51 L C -1.9067
52 E C -2.2450
53 G C -2.2230
54 E C -2.6634
55 V C 0.0000
56 R C -2.7977
57 S C -2.2459
58 L C 0.0000
59 L C -2.5469
60 K C -3.1212
61 D C -2.8312
62 I C 0.0000
63 S C -2.1493
64 Q C -2.1080
65 K C -1.5801
66 V C 0.0000
67 A C -0.5500
68 V C -0.0540
69 Y C -0.6178
70 S C -0.8445
71 T C -0.5594
72 C C -0.8940
73 R C -2.0653
1 D D -2.4881
2 T D -2.0177
3 K D -2.8505 mutated: VK3D
4 D D -2.4380
5 L D -1.9288
6 N D -3.1559
7 K D -2.8507
8 L D 0.0000
9 N D -3.1078
10 E D -3.3764
11 I D 0.0000
12 E D -2.4642
13 G D -2.3198
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 -3.4416
31 V D 0.0000
32 S D -3.2187
33 D D -4.3016
34 L D 0.0000
35 E D -3.6834
36 N D -4.2063
37 E D -4.3415
38 A D 0.0000
39 K D -4.4089
40 K D -3.9572
41 Q D -3.1787
42 E D -3.0884
43 A D -2.0151
44 A D -1.6980
45 I D 0.0000
46 M D -1.1304
47 D D -2.4717
48 Y D -1.8669
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 -3.4573
64 D D -3.5230
65 I D -2.3630
66 R D -2.6949
67 K D -2.7168
68 T D -1.2600
69 L D -0.8153
70 P D -0.3070
71 S D -0.5180
72 G D -0.4639
73 C D -0.8835
74 H D -1.6878
75 N D -2.1334
76 T D -0.9772
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 -1.8371 1.5632 View CSV PDB
4.5 -1.9563 1.3751 View CSV PDB
5.0 -2.1035 1.1793 View CSV PDB
5.5 -2.2503 1.026 View CSV PDB
6.0 -2.366 0.9606 View CSV PDB
6.5 -2.4291 0.995 View CSV PDB
7.0 -2.4377 1.0991 View CSV PDB
7.5 -2.4081 1.2358 View CSV PDB
8.0 -2.3569 1.3843 View CSV PDB
8.5 -2.2905 1.5354 View CSV PDB
9.0 -2.2074 1.6835 View CSV PDB