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

Status: done

Started: 2025-05-06 18:06:00
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNAHLALSASIGRVRELCAQARGAASKVKV
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 HK55B
Energy difference between WT (input) and mutated protein (by FoldX) -0.982103 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                                                       (00:02:14)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:41)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/154c6c643b84a9c/tmp/folded.pdb                (00:02:41)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:54)
Show buried residues
Minimal score value
-4.4347
Maximal score value
1.0245
Average score
-1.5994
Total score value
-377.46
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 -0.0333
42 K B -0.4321
43 L B 0.0000
44 S B -0.2729
45 I B 0.7152
46 L B 0.0000
47 E B -2.1057
48 N B -1.4763
49 R B -0.8859
50 G B -0.4503
51 V B 0.8902
52 H B -0.2555
53 N B -0.7985
54 A B 0.0000
55 K B -0.1919 mutated: HK55B
56 L B 1.0245
57 A B 0.1341
58 L B 0.0000
59 S B 0.0118
60 A B -0.1068
61 S B -0.7569
62 I B 0.0000
63 G B -1.8822
64 R B -2.3796
65 V B 0.0000
66 R B -2.8086
67 E B -3.2108
68 L B 0.0000
69 C B 0.0000
70 A B -1.9400
71 Q B -2.1764
72 A B 0.0000
73 R B -2.3307
74 G B -1.6402
75 A B -1.7392
76 A B -1.4526
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 -2.2944
29 D C -2.4733
30 L C 0.0000
31 E C -2.8990
32 R C -4.1855
33 K C -4.0428
34 Y C 0.0000
35 E C -4.4347
36 D C -4.3755
37 N C -3.3446
38 Q C -3.2314
39 R C -3.6401
40 Y C -2.1650
41 L C 0.0000
42 E C -2.9296
43 D C -2.5636
44 K C -2.1787
45 A C -1.7910
46 Q C -2.3978
47 E C -2.4228
48 L C 0.0000
49 A C -1.8940
50 R C -2.7913
51 L C -1.9360
52 E C -2.2827
53 G C -2.2434
54 E C -2.6825
55 V C 0.0000
56 R C -2.8535
57 S C -2.2765
58 L C 0.0000
59 L C -2.5635
60 K C -3.1397
61 D C -2.8451
62 I C 0.0000
63 S C -2.1474
64 Q C -2.1099
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 -1.0141
26 D D -1.8857
27 L D 0.0000
28 D D -3.6199
29 R D -3.8628
30 K D -3.4403
31 V D 0.0000
32 S D -3.2127
33 D D -4.2923
34 L D 0.0000
35 E D -3.6649
36 N D -4.1753
37 E D -4.3008
38 A D 0.0000
39 K D -4.3785
40 K D -3.9211
41 Q D -3.1850
42 E D -3.0662
43 A D -2.0111
44 A D -1.7619
45 I D 0.0000
46 M D -1.1650
47 D D -2.5004
48 Y D -1.9676
49 N D -2.0590
50 R D -3.3942
51 D D -3.0563
52 I D 0.0000
53 E D -3.2982
54 E D -3.4193
55 I D 0.0000
56 M D -2.1496
57 K D -2.9338
58 C D -2.4690
59 I D 0.0000
60 R D -3.4774
61 N D -3.0551
62 L D 0.0000
63 E D -3.4561
64 D D -3.5223
65 I D -2.3614
66 R D -2.6952
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 -1.658 1.6484 View CSV PDB
4.5 -1.775 1.5869 View CSV PDB
5.0 -1.921 1.4887 View CSV PDB
5.5 -2.0686 1.371 View CSV PDB
6.0 -2.1888 1.3202 View CSV PDB
6.5 -2.2606 1.3694 View CSV PDB
7.0 -2.281 1.4332 View CSV PDB
7.5 -2.264 1.5048 View CSV PDB
8.0 -2.2255 1.5796 View CSV PDB
8.5 -2.172 1.6553 View CSV PDB
9.0 -2.1016 1.7309 View CSV PDB