Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: DK47D]

Status: done

Started: 2025-05-14 01:59:46
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 DK47D
Energy difference between WT (input) and mutated protein (by FoldX) -0.767423 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                                                       (00:03:50)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:05:05)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/536fbe553cc7e27/tmp/folded.pdb                (00:05:05)
[INFO]       Main:     Simulation completed successfully.                                          (00:09:12)
Show buried residues
Minimal score value
-4.3722
Maximal score value
1.2407
Average score
-1.5754
Total score value
-371.7903
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 -0.8867
50 G B -0.4727
51 V B 0.9250
52 H B -0.2234
53 N B -0.6887
54 A B 0.0000
55 S B 0.2519
56 L B 1.2407
57 A B 0.2625
58 L B 0.0000
59 S B 0.1654
60 A B -0.0439
61 S B -0.6314
62 I B 0.0000
63 G B -1.6565
64 R B -2.2039
65 V B 0.0000
66 R B -2.1800
67 E B -2.9170
68 L B 0.0000
69 C B 0.0000
70 A B -1.7544
71 Q B -2.0161
72 A B 0.0000
73 R B -2.3008
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 -2.4883
30 L C 0.0000
31 E C -2.8997
32 R C -4.1703
33 K C -4.0249
34 Y C 0.0000
35 E C -4.3720
36 D C -4.3227
37 N C -3.2954
38 Q C -3.0448
39 R C -3.5981
40 Y C -2.1434
41 L C 0.0000
42 E C -2.8933
43 D C -2.6029
44 K C -2.1244
45 A C -1.6967
46 Q C -2.2917
47 E C -2.3799
48 L C 0.0000
49 A C -1.8480
50 R C -2.7537
51 L C -1.9161
52 E C -2.1989
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 -3.1980
33 D D -4.2720
34 L D 0.0000
35 E D -3.6403
36 N D -4.1400
37 E D -4.2522
38 A D 0.0000
39 K D -4.3722
40 K D -3.9170
41 Q D -3.1318
42 E D -3.0551
43 A D -1.9716
44 A D -1.6608
45 I D 0.0000
46 M D -1.0059
47 K D -2.2876 mutated: DK47D
48 Y D -1.7060
49 N D -1.8548
50 R D -3.1071
51 D D -2.5656
52 I D 0.0000
53 E D -3.1295
54 E D -3.1531
55 I D 0.0000
56 M D -2.2110
57 K D -3.2162
58 C D -2.5286
59 I D 0.0000
60 R D -3.5947
61 N D -3.1591
62 L D 0.0000
63 E D -3.4957
64 D D -3.5212
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 -1.6985 1.6489 View CSV PDB
4.5 -1.8103 1.6401 View CSV PDB
5.0 -1.9486 1.6458 View CSV PDB
5.5 -2.0856 1.6575 View CSV PDB
6.0 -2.1913 1.6735 View CSV PDB
6.5 -2.2455 1.6873 View CSV PDB
7.0 -2.2477 1.6951 View CSV PDB
7.5 -2.2134 1.6983 View CSV PDB
8.0 -2.1587 1.6994 View CSV PDB
8.5 -2.09 1.6998 View CSV PDB
9.0 -2.0061 1.6999 View CSV PDB