Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: DK47D] [mutate: KD47D, DK4D]

Status: done

Started: 2025-05-15 16:28:04
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 DK4D,KD47D
Energy difference between WT (input) and mutated protein (by FoldX) -1.15456 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                                                       (00:01:56)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:37)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/1b1b41536e139a9/tmp/folded.pdb                (00:02:37)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:55)
Show buried residues
Minimal score value
-4.3818
Maximal score value
1.2429
Average score
-1.5794
Total score value
-372.7282
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 -2.4594
9 Q B -2.0403
10 Y B -1.5830
11 E B -2.8495
12 G B -1.9184
13 L B -0.9596
14 R B -2.6110
15 G B -2.6916
16 Q B -2.2601
17 D B -2.2917
18 L B -2.3683
19 G B 0.0000
20 Q B -1.7867
21 A B 0.0000
22 V B 0.0000
23 L B -0.2315
24 D B -1.2364
25 A B 0.0000
26 G B -1.0818
27 H B -1.3635
28 S B -1.4613
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 -0.2696
45 I B 0.7213
46 L B 0.0000
47 E B -2.0984
48 N B -1.4647
49 R B -0.8776
50 G B -0.4653
51 V B 0.9316
52 H B -0.2130
53 N B -0.6860
54 A B 0.0000
55 S B 0.2561
56 L B 1.2429
57 A B 0.2608
58 L B 0.0000
59 S B 0.1378
60 A B -0.0454
61 S B -0.6318
62 I B 0.0000
63 G B -1.6889
64 R B -2.2054
65 V B 0.0000
66 R B -2.2164
67 E B -2.9333
68 L B 0.0000
69 C B 0.0000
70 A B -1.7922
71 Q B -2.0980
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 -2.8272
2 A C -2.3169
3 R C -3.3169
4 R C -3.4524
5 K C -2.7441
6 A C 0.0000
7 E C -2.4925
8 M C -1.5932
9 L C 0.0000
10 Q C -2.2013
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 -2.0982
45 A C -1.6807
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 -2.1985
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 -1.3339
2 T D -0.3417
3 V D 0.5933
4 K D -0.8331 mutated: DK4D
5 L D -0.8095
6 N D -1.9844
7 K D -1.9281
8 L D 0.0000
9 N D -3.0968
10 E D -3.3583
11 I D 0.0000
12 E D -2.4531
13 G D -2.3109
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 -3.2057
33 D D -4.2793
34 L D 0.0000
35 E D -3.6556
36 N D -4.1605
37 E D -4.2690
38 A D 0.0000
39 K D -4.3818
40 K D -3.9255
41 Q D -3.1462
42 E D -3.0666
43 A D -1.9928
44 A D -1.6833
45 I D 0.0000
46 M D -1.0832
47 D D -2.4386 mutated: KD47D
48 Y D -1.8166
49 N D -1.9622
50 R D -3.2760
51 D D -2.8794
52 I D 0.0000
53 E D -3.2329
54 E D -3.2533
55 I D 0.0000
56 M D -2.2546
57 K D -3.2475
58 C D -2.5273
59 I D 0.0000
60 R D -3.5952
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 -1.6562 1.6615 View CSV PDB
4.5 -1.7728 1.646 View CSV PDB
5.0 -1.9179 1.6509 View CSV PDB
5.5 -2.0637 1.6615 View CSV PDB
6.0 -2.1804 1.6767 View CSV PDB
6.5 -2.2475 1.6906 View CSV PDB
7.0 -2.263 1.6988 View CSV PDB
7.5 -2.2419 1.7023 View CSV PDB
8.0 -2.2001 1.7035 View CSV PDB
8.5 -2.1435 1.7039 View CSV PDB
9.0 -2.0708 1.704 View CSV PDB