Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: LT56B] [mutate: IK45B] [mutate: VK3D] [mutate: TL56B]

Status: done

Started: 2025-04-25 13:54:39
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNASTALSASIGRVRELCAQARGAASKVKV
D: DTKDLNKLNEIEGTLNKAKDEMKVSDLDRKVSDLENEAKKQEAAIMDYNRDIEEIMKCIRNLEDIRKTLPSGCHNTPSIEKP
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 TL56B
Energy difference between WT (input) and mutated protein (by FoldX) -0.14997 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                                                       (00:01:43)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:46)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/1e7bd9b132e69e1/tmp/folded.pdb                (00:01:46)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:53)
Show buried residues
Minimal score value
-4.429
Maximal score value
1.2444
Average score
-1.691
Total score value
-399.0741
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 -2.4674
9 Q B -2.0528
10 Y B -1.6049
11 E B -2.8831
12 G B -1.9511
13 L B -1.0148
14 R B -2.7222
15 G B -2.7605
16 Q B -2.3271
17 D B -2.3288
18 L B -2.3815
19 G B -1.7911
20 Q B -1.7617
21 A B 0.0000
22 V B 0.0000
23 L B -0.0251
24 D B -1.1187
25 A B 0.0000
26 G B -1.0125
27 H B -1.2977
28 S B -1.4240
29 V B 0.0000
30 S B -1.3329
31 T B -1.4047
32 L B 0.0000
33 E B -2.3456
34 K B -2.3659
35 T B -1.4950
36 L B 0.0000
37 P B -1.2926
38 Q B -1.3585
39 L B 0.0000
40 L B -0.5542
41 A B -0.9686
42 K B -1.6788
43 L B 0.0000
44 S B -2.0422
45 K B -2.9686
46 L B 0.0000
47 E B -3.2587
48 N B -2.6698
49 R B -1.8670
50 G B -0.8589
51 V B 0.9272
52 H B -0.1940
53 N B -0.6630
54 A B 0.0000
55 S B 0.2826
56 L B 1.2444 mutated: TL56B
57 A B 0.2850
58 L B 0.0000
59 S B 0.1348
60 A B -0.0393
61 S B -0.7011
62 I B 0.0000
63 G B -1.8687
64 R B -2.3554
65 V B 0.0000
66 R B -2.7847
67 E B -3.2025
68 L B 0.0000
69 C B 0.0000
70 A B -1.9481
71 Q B -2.1992
72 A B 0.0000
73 R B -2.3416
74 G B -1.6533
75 A B -1.7477
76 A B -1.4572
77 S B -1.6388
78 K B -2.2342
79 V B 0.0000
80 K B -1.2777
81 V B 0.6642
1 D C -2.8246
2 A C -2.2973
3 R C -3.3122
4 R C -3.4356
5 K C -2.7287
6 A C 0.0000
7 E C -2.4561
8 M C -1.5635
9 L C 0.0000
10 Q C -2.1562
11 N C -2.4593
12 E C -1.9671
13 A C 0.0000
14 K C -2.3353
15 T C -1.5607
16 L C -1.0339
17 L C -1.3431
18 A C -0.9505
19 Q C -1.2562
20 A C 0.0000
21 N C -1.4066
22 S C -1.1779
23 K C -1.4513
24 L C -1.2651
25 Q C -1.6306
26 L C -1.2941
27 L C 0.0000
28 K C -2.3241
29 D C -2.5208
30 L C 0.0000
31 E C -3.5186
32 R C -4.2417
33 K C -4.0728
34 Y C 0.0000
35 E C -4.4290
36 D C -4.3424
37 N C -3.3043
38 Q C -3.0393
39 R C -3.5537
40 Y C -2.0922
41 L C 0.0000
42 E C -2.7217
43 D C -2.4916
44 K C -2.0524
45 A C -1.6249
46 Q C -2.2446
47 E C -2.3506
48 L C 0.0000
49 A C -1.8462
50 R C -2.7553
51 L C -1.9072
52 E C -2.2453
53 G C -2.2225
54 E C -2.6627
55 V C 0.0000
56 R C -2.7970
57 S C -2.2455
58 L C 0.0000
59 L C -2.5452
60 K C -3.1215
61 D C -2.8345
62 I C 0.0000
63 S C -2.1491
64 Q C -2.1077
65 K C -1.5782
66 V C 0.0000
67 A C -0.5495
68 V C -0.0529
69 Y C -0.6170
70 S C -0.8440
71 T C -0.5591
72 C C -0.8940
73 R C -2.0653
1 D D -2.4894
2 T D -2.0206
3 K D -2.8544
4 D D -2.4407
5 L D -1.9366
6 N D -3.1629
7 K D -2.8583
8 L D 0.0000
9 N D -3.1121
10 E D -3.3804
11 I D 0.0000
12 E D -2.4653
13 G D -2.3208
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 -3.4416
31 V D 0.0000
32 S D -3.2199
33 D D -4.3039
34 L D 0.0000
35 E D -3.6861
36 N D -4.2104
37 E D -4.3499
38 A D 0.0000
39 K D -4.4117
40 K D -3.9602
41 Q D -3.1796
42 E D -3.0896
43 A D -2.0160
44 A D -1.6978
45 I D 0.0000
46 M D -1.1304
47 D D -2.4717
48 Y D -1.8667
49 N D -2.0161
50 R D -3.3552
51 D D -3.0247
52 I D 0.0000
53 E D -3.2368
54 E D -3.3790
55 I D 0.0000
56 M D -2.1328
57 K D -2.9293
58 C D -2.4614
59 I D 0.0000
60 R D -3.4808
61 N D -3.0591
62 L D 0.0000
63 E D -3.4575
64 D D -3.5230
65 I D -2.3630
66 R D -2.6951
67 K D -2.7168
68 T D -1.2600
69 L D -0.8146
70 P D -0.3064
71 S D -0.5173
72 G D -0.4635
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
View in 3Dmol

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 -1.8093 1.6488 View CSV PDB
4.5 -1.9276 1.6512 View CSV PDB
5.0 -2.0736 1.6573 View CSV PDB
5.5 -2.2186 1.669 View CSV PDB
6.0 -2.332 1.6841 View CSV PDB
6.5 -2.393 1.6964 View CSV PDB
7.0 -2.4009 1.703 View CSV PDB
7.5 -2.371 1.7056 View CSV PDB
8.0 -2.3197 1.7065 View CSV PDB
8.5 -2.253 1.7068 View CSV PDB
9.0 -2.1697 1.7069 View CSV PDB