Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: SH55B]

Status: done

Started: 2025-05-06 17:24:44
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
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 SH55B
Energy difference between WT (input) and mutated protein (by FoldX) 1.88578 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
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                                                       (00:02:12)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:21)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/87c4327b9f4b1/tmp/folded.pdb                  (00:02:21)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:42)
Show buried residues
Minimal score value
-4.3567
Maximal score value
1.219
Average score
-1.5836
Total score value
-373.7413
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 -2.9710
5 R B -3.2802
6 W B -1.2863
7 Q B -1.9316
8 G B -2.4558
9 Q B -2.0406
10 Y B -1.5815
11 E B -2.8458
12 G B -1.9186
13 L B -0.9570
14 R B -2.5854
15 G B -2.7059
16 Q B -2.2811
17 D B -2.2820
18 L B -2.3506
19 G B -1.3671
20 Q B -1.7488
21 A B 0.0000
22 V B 0.0000
23 L B -0.1431
24 D B -1.2138
25 A B 0.0000
26 G B -1.0514
27 H B -1.3479
28 S B -1.4558
29 V B 0.0000
30 S B -1.3354
31 T B -1.4052
32 L B 0.0000
33 E B -2.3482
34 K B -2.3776
35 T B -1.5153
36 L B 0.0000
37 P B -1.3197
38 Q B -1.4191
39 L B 0.0000
40 L B -0.0634
41 A B -0.0358
42 K B -0.4383
43 L B 0.0000
44 S B -0.2783
45 I B 0.7075
46 L B 0.0000
47 E B -2.1167
48 N B -1.4753
49 R B -0.8629
50 G B -0.4311
51 V B 0.9728
52 H B -0.1067
53 N B -0.6464
54 A B 0.0000
55 H B 0.2157 mutated: SH55B
56 L B 1.2190
57 A B 0.2657
58 L B 0.0000
59 S B 0.1113
60 A B -0.0571
61 S B -0.7215
62 I B 0.0000
63 G B -1.8839
64 R B -2.3858
65 V B 0.0000
66 R B -2.7989
67 E B -3.1909
68 L B 0.0000
69 C B 0.0000
70 A B -1.8996
71 Q B -2.0939
72 A B 0.0000
73 R B -2.3011
74 G B -1.6054
75 A B -1.7145
76 A B -1.4390
77 S B -1.6243
78 K B -2.2326
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.8201
2 A C -2.2895
3 R C -3.2812
4 R C -3.4369
5 K C -2.7300
6 A C 0.0000
7 E C -2.4823
8 M C -1.5775
9 L C 0.0000
10 Q C -2.1927
11 N C -2.4754
12 E C -1.9765
13 A C 0.0000
14 K C -2.3508
15 T C -1.5667
16 L C -1.0367
17 L C -1.3468
18 A C -0.9520
19 Q C -1.2529
20 A C 0.0000
21 N C -1.4132
22 S C -1.1823
23 K C -1.4622
24 L C -1.2859
25 Q C -1.6287
26 L C -1.2867
27 L C 0.0000
28 K C -2.3091
29 D C -2.4788
30 L C 0.0000
31 E C -2.8756
32 R C -4.1490
33 K C -4.0049
34 Y C 0.0000
35 E C -4.3164
36 D C -4.2983
37 N C -3.2732
38 Q C -3.0601
39 R C -3.5789
40 Y C -2.1174
41 L C 0.0000
42 E C -2.7849
43 D C -2.5514
44 K C -2.0945
45 A C -1.6587
46 Q C -2.2584
47 E C -2.3618
48 L C 0.0000
49 A C -1.8480
50 R C -2.7537
51 L C -1.9161
52 E C -2.2700
53 G C -2.2460
54 E C -2.6847
55 V C 0.0000
56 R C -2.8525
57 S C -2.2796
58 L C 0.0000
59 L C -2.5464
60 K C -3.1408
61 D C -2.8460
62 I C 0.0000
63 S C -2.1372
64 Q C -2.1109
65 K C -1.5840
66 V C 0.0000
67 A C -0.5510
68 V C -0.0537
69 Y C -0.6176
70 S C -0.8439
71 T C -0.5597
72 C C -0.8939
73 R C -2.0661
1 D D -1.3058
2 T D -0.2942
3 V D 0.6606
4 D D -0.6876
5 L D -0.7385
6 N D -1.9307
7 K D -1.8574
8 L D 0.0000
9 N D -3.0718
10 E D -3.3384
11 I D 0.0000
12 E D -2.4525
13 G D -2.3115
14 T D -2.1628
15 L D 0.0000
16 N D -2.4355
17 K D -3.3493
18 A D 0.0000
19 K D -2.5872
20 D D -3.2249
21 E D -2.5283
22 M D -1.9425
23 K D -2.3823
24 V D -0.0583
25 S D -1.0124
26 D D -1.8823
27 L D 0.0000
28 D D -3.6200
29 R D -3.8609
30 K D -3.4394
31 V D 0.0000
32 S D -3.1992
33 D D -4.2741
34 L D 0.0000
35 E D -3.6368
36 N D -4.1352
37 E D -4.2443
38 A D 0.0000
39 K D -4.3567
40 K D -3.8970
41 Q D -3.1140
42 E D -3.0476
43 A D -1.9898
44 A D -1.6897
45 I D 0.0000
46 M D -1.1191
47 D D -2.4599
48 Y D -1.8710
49 N D -2.0128
50 R D -3.3531
51 D D -3.0155
52 I D 0.0000
53 E D -3.2385
54 E D -3.3955
55 I D 0.0000
56 M D -2.1273
57 K D -2.9113
58 C D -2.4589
59 I D 0.0000
60 R D -3.4741
61 N D -3.0512
62 L D 0.0000
63 E D -3.4538
64 D D -3.5215
65 I D -2.3598
66 R D -2.6944
67 K D -2.7156
68 T D -1.2586
69 L D -0.8144
70 P D -0.3057
71 S D -0.5168
72 G D -0.4613
73 C D -0.8821
74 H D -1.6890
75 N D -2.1385
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
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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 -1.6353 1.6499 View CSV PDB
4.5 -1.7513 1.6428 View CSV PDB
5.0 -1.8963 1.6646 View CSV PDB
5.5 -2.0433 1.6868 View CSV PDB
6.0 -2.1633 1.7043 View CSV PDB
6.5 -2.2357 1.7151 View CSV PDB
7.0 -2.2576 1.7201 View CSV PDB
7.5 -2.2427 1.722 View CSV PDB
8.0 -2.2067 1.7226 View CSV PDB
8.5 -2.1557 1.7228 View CSV PDB
9.0 -2.0879 1.7229 View CSV PDB