Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: SH55B] [mutate: HK55B] [mutate: LS56B]

Status: done

Started: 2025-05-06 18:22:14
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNAKLALSASIGRVRELCAQARGAASKVKV
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 LS56B
Energy difference between WT (input) and mutated protein (by FoldX) 0.422917 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                                                       (00:02:02)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:15)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/a842508ab7a781f/tmp/folded.pdb                (00:02:15)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:39)
Show buried residues
Minimal score value
-4.4303
Maximal score value
0.7126
Average score
-1.6095
Total score value
-379.8322
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 -2.7671
16 Q B -2.3344
17 D B -2.3413
18 L B -2.3879
19 G B -1.3807
20 Q B -1.7745
21 A B 0.0000
22 V B 0.0000
23 L B -0.0398
24 D B -1.1439
25 A B 0.0000
26 G B -1.0081
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 -2.3545
34 K B -2.3823
35 T B -1.5206
36 L B 0.0000
37 P B -1.3269
38 Q B -1.4314
39 L B 0.0000
40 L B -0.0685
41 A B -0.0412
42 K B -0.4379
43 L B 0.0000
44 S B -0.2836
45 I B 0.6962
46 L B 0.0000
47 E B -2.1121
48 N B -1.4830
49 R B -0.8827
50 G B -0.4396
51 V B 0.7126
52 H B -0.4780
53 N B -1.3462
54 A B 0.0000
55 K B -1.0345
56 S B -0.7211 mutated: LS56B
57 A B -0.7178
58 L B 0.0000
59 S B -0.5831
60 A B -0.5587
61 S B -0.9974
62 I B 0.0000
63 G B -1.8663
64 R B -2.3543
65 V B 0.0000
66 R B -2.7843
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 -2.2936
3 R C -3.3136
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 -0.9502
19 Q C -1.2558
20 A C 0.0000
21 N C -1.4143
22 S C -1.1793
23 K C -1.4525
24 L C -1.2799
25 Q C -1.6195
26 L C -1.2769
27 L C 0.0000
28 K C -2.2872
29 D C -2.4776
30 L C 0.0000
31 E C -2.8906
32 R C -4.1794
33 K C -4.0214
34 Y C 0.0000
35 E C -4.4303
36 D C -4.3717
37 N C -3.3101
38 Q C -3.1969
39 R C -3.6362
40 Y C -2.1653
41 L C 0.0000
42 E C -2.9156
43 D C -2.5507
44 K C -2.1714
45 A C -1.9788
46 Q C -2.3940
47 E C -2.4197
48 L C 0.0000
49 A C -1.8928
50 R C -2.7913
51 L C -1.9273
52 E C -2.2606
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 -1.3005
2 T D -0.2938
3 V D 0.6604
4 D D -0.6793
5 L D -0.7374
6 N D -1.9293
7 K D -1.8423
8 L D 0.0000
9 N D -3.0704
10 E D -3.3369
11 I D 0.0000
12 E D -2.4493
13 G D -2.3091
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 -3.4417
31 V D 0.0000
32 S D -3.2236
33 D D -4.3107
34 L D 0.0000
35 E D -3.6736
36 N D -4.1936
37 E D -4.3198
38 A D 0.0000
39 K D -4.3534
40 K D -3.8723
41 Q D 0.0000
42 E D -3.0021
43 A D -1.9674
44 A D -1.7015
45 I D 0.0000
46 M D -1.1404
47 D D -2.4781
48 Y D -1.9483
49 N D -2.0536
50 R D -3.3878
51 D D -3.0480
52 I D 0.0000
53 E D -3.2938
54 E D -3.4064
55 I D 0.0000
56 M D -2.1516
57 K D -2.9423
58 C D -2.4688
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 -1.6826 1.6192 View CSV PDB
4.5 -1.7991 1.5574 View CSV PDB
5.0 -1.9441 1.4594 View CSV PDB
5.5 -2.0903 1.3428 View CSV PDB
6.0 -2.2088 1.2324 View CSV PDB
6.5 -2.2792 1.1483 View CSV PDB
7.0 -2.2993 1.105 View CSV PDB
7.5 -2.2831 1.2358 View CSV PDB
8.0 -2.2459 1.3843 View CSV PDB
8.5 -2.1938 1.5354 View CSV PDB
9.0 -2.1249 1.6835 View CSV PDB