Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: DK47D] [mutate: DK33D]

Status: done

Started: 2025-05-14 02:18:31
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNASLALSASIGRVRELCAQARGAASKVKV
D: DTVDLNKLNEIEGTLNKAKDEMKVSDLDRKVSDLENEAKKQEAAIMKYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
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 DK33D
Energy difference between WT (input) and mutated protein (by FoldX) -1.00475 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                                                       (00:01:54)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:29)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/22dd683efa55a95/tmp/folded.pdb                (00:02:29)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:47)
Show buried residues
Minimal score value
-4.3866
Maximal score value
1.2429
Average score
-1.5733
Total score value
-371.2983
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 -2.9704
5 R B -3.2794
6 W B -1.2847
7 Q B -1.9296
8 G B -2.4602
9 Q B -2.0432
10 Y B -1.5875
11 E B -2.8553
12 G B -1.9248
13 L B -0.9737
14 R B -2.6302
15 G B -2.7076
16 Q B -2.2862
17 D B -2.2905
18 L B -2.3561
19 G B -1.3623
20 Q B -1.7443
21 A B 0.0000
22 V B 0.0000
23 L B -0.1039
24 D B -1.1828
25 A B 0.0000
26 G B -1.0341
27 H B -1.3324
28 S B -1.4450
29 V B 0.0000
30 S B -1.3337
31 T B -1.4042
32 L B 0.0000
33 E B -2.3485
34 K B -2.3784
35 T B -1.5166
36 L B 0.0000
37 P B -1.3216
38 Q B -1.4231
39 L B 0.0000
40 L B -0.0626
41 A B -0.0270
42 K B -0.4236
43 L B 0.0000
44 S B -0.2407
45 I B 0.7404
46 L B 0.0000
47 E B -2.0152
48 N B -1.4350
49 R B -0.8587
50 G B -0.4564
51 V B 0.9316
52 H B -0.2130
53 N B -0.6860
54 A B 0.0000
55 S B 0.2503
56 L B 1.2429
57 A B 0.2608
58 L B 0.0000
59 S B 0.1648
60 A B -0.0454
61 S B -0.6314
62 I B 0.0000
63 G B -1.6534
64 R B -2.2046
65 V B 0.0000
66 R B -2.1770
67 E B -2.9321
68 L B 0.0000
69 C B 0.0000
70 A B -1.7916
71 Q B -2.0977
72 A B 0.0000
73 R B -2.3303
74 G B -1.6400
75 A B -1.7390
76 A B -1.4525
77 S B -1.6346
78 K B -2.2337
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.8229
2 A C -2.2957
3 R C -3.2955
4 R C -3.4451
5 K C -2.7394
6 A C 0.0000
7 E C -2.4890
8 M C -1.5909
9 L C 0.0000
10 Q C -2.1877
11 N C -2.4759
12 E C -1.9772
13 A C 0.0000
14 K C -2.3450
15 T C -1.5646
16 L C -1.0365
17 L C -1.3454
18 A C -0.9524
19 Q C -1.2570
20 A C 0.0000
21 N C -1.4134
22 S C -1.1802
23 K C -1.4524
24 L C -1.2790
25 Q C -1.6205
26 L C -1.2768
27 L C 0.0000
28 K C -2.2937
29 D C -2.4719
30 L C 0.0000
31 E C -2.8949
32 R C -4.1645
33 K C -4.0175
34 Y C 0.0000
35 E C -4.3717
36 D C -4.3254
37 N C -3.2940
38 Q C -3.0452
39 R C -3.5978
40 Y C -2.1389
41 L C 0.0000
42 E C -2.8960
43 D C -2.5700
44 K C -2.1050
45 A C -1.6855
46 Q C -2.2734
47 E C -2.3507
48 L C 0.0000
49 A C -1.8370
50 R C -2.7467
51 L C -1.9128
52 E C -2.1982
53 G C -2.2499
54 E C -2.6884
55 V C 0.0000
56 R C -2.8704
57 S C -2.2848
58 L C 0.0000
59 L C -2.5684
60 K C -3.1437
61 D C -2.8471
62 I C 0.0000
63 S C -2.1471
64 Q C -2.1097
65 K C -1.5809
66 V C 0.0000
67 A C -0.5503
68 V C -0.0528
69 Y C -0.6160
70 S C -0.8431
71 T C -0.5587
72 C C -0.8927
73 R C -2.0648
1 D D -1.3025
2 T D -0.2958
3 V D 0.6573
4 D D -0.6893
5 L D -0.7401
6 N D -1.9314
7 K D -1.8542
8 L D 0.0000
9 N D -3.0713
10 E D -3.3376
11 I D 0.0000
12 E D -2.4506
13 G D -2.3091
14 T D -2.1609
15 L D 0.0000
16 N D -2.4320
17 K D -3.3473
18 A D 0.0000
19 K D -2.5846
20 D D -3.2235
21 E D -2.5278
22 M D -1.9424
23 K D -2.3827
24 V D -0.0591
25 S D -1.0042
26 D D -1.8680
27 L D 0.0000
28 D D -3.5855
29 R D -3.8050
30 K D -3.3346
31 V D 0.0000
32 S D -3.1465
33 K D -4.1709 mutated: DK33D
34 L D 0.0000
35 E D -3.6359
36 N D -4.1629
37 E D -4.2646
38 A D 0.0000
39 K D -4.3866
40 K D -3.9347
41 Q D -3.1413
42 E D -3.0609
43 A D -1.9721
44 A D -1.6604
45 I D 0.0000
46 M D -1.0054
47 K D -2.2869
48 Y D -1.7062
49 N D -1.8550
50 R D -3.1073
51 D D -2.5626
52 I D 0.0000
53 E D -3.1317
54 E D -3.1565
55 I D 0.0000
56 M D -2.2131
57 K D -3.2186
58 C D -2.5286
59 I D 0.0000
60 R D -3.5958
61 N D -3.1598
62 L D 0.0000
63 E D -3.4965
64 D D -3.5221
65 I D -2.3614
66 R D -2.6950
67 K D -2.7161
68 T D -1.2592
69 L D -0.8141
70 P D -0.3051
71 S D -0.5161
72 G D -0.4602
73 C D -0.8803
74 H D -1.6860
75 N D -2.1324
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 -1.7475 1.6726 View CSV PDB
4.5 -1.8531 1.646 View CSV PDB
5.0 -1.9848 1.6511 View CSV PDB
5.5 -2.1148 1.6617 View CSV PDB
6.0 -2.2125 1.677 View CSV PDB
6.5 -2.2568 1.6908 View CSV PDB
7.0 -2.2471 1.6989 View CSV PDB
7.5 -2.2001 1.7023 View CSV PDB
8.0 -2.1328 1.7035 View CSV PDB
8.5 -2.0524 1.7039 View CSV PDB
9.0 -1.9588 1.704 View CSV PDB