Project name: phlamhtrimer [mutate: LR73C, FH74D] [mutate: LT56B] [mutate: IK45B] [mutate: VK3D] [mutate: TL56B] [mutate: LS56B] [mutate: SL56B, NA53B] [mutate: AN53B] [mutate: SK55B] [mutate: KR55B] [mutate: RH55B]

Status: done

Started: 2025-04-25 14:34:18
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNARLALSASIGRVRELCAQARGAASKVKV
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 RH55B
Energy difference between WT (input) and mutated protein (by FoldX) 5.29325 kcal/mol

CAUTION: Your mutation/s can destabilize the protein structure
Downloads Download all the data
Simulation log 
[INFO]       Logger:   Verbosity set to: 2 - [INFO]                                                (00:00:00)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:00)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with all chain(s) selected           (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[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                                          (00:02:14)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/b5b398d2fdaf75/tmp/folded.pdb                 (00:02:14)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:42)
Show buried residues
Minimal score value
-4.4251
Maximal score value
1.1134
Average score
-1.6952
Total score value
-400.0779
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 -2.7609
16 Q B -2.3271
17 D B -2.3268
18 L B -2.3788
19 G B -1.7850
20 Q B -1.7536
21 A B 0.0000
22 V B 0.0000
23 L B -0.0015
24 D B -1.1042
25 A B 0.0000
26 G B -0.9998
27 H B -1.2898
28 S B -1.4196
29 V B 0.0000
30 S B -1.3317
31 T B -1.4042
32 L B 0.0000
33 E B -2.3460
34 K B -2.3667
35 T B -1.4962
36 L B 0.0000
37 P B -1.2943
38 Q B -1.3620
39 L B 0.0000
40 L B -0.5552
41 A B -0.9697
42 K B -1.6797
43 L B 0.0000
44 S B -2.0409
45 K B -2.9672
46 L B 0.0000
47 E B -3.2561
48 N B -2.6657
49 R B -1.8282
50 G B -0.7999
51 V B 0.9746
52 H B -0.1716
53 N B -0.7790
54 A B 0.0000
55 H B -0.1446 mutated: RH55B
56 L B 1.1134
57 A B 0.1103
58 L B 0.0000
59 S B 0.0284
60 A B -0.0792
61 S B -0.7314
62 I B 0.0000
63 G B -1.8669
64 R B -2.3551
65 V B 0.0000
66 R B -2.8039
67 E B -3.2311
68 L B 0.0000
69 C B 0.0000
70 A B -1.9955
71 Q B -2.2947
72 A B 0.0000
73 R B -2.3714
74 G B -1.6875
75 A B -1.7729
76 A B -1.4648
77 S B -1.6490
78 K B -2.2344
79 V B 0.0000
80 K B -1.2777
81 V B 0.6643
1 D C -2.8246
2 A C -2.2978
3 R C -3.3125
4 R C -3.4357
5 K C -2.7288
6 A C 0.0000
7 E C -2.4558
8 M C -1.5637
9 L C 0.0000
10 Q C -2.1533
11 N C -2.4593
12 E C -1.9674
13 A C 0.0000
14 K C -2.3355
15 T C -1.5608
16 L C -1.0340
17 L C -1.3431
18 A C -0.9505
19 Q C -1.2562
20 A C 0.0000
21 N C -1.4070
22 S C -1.1774
23 K C -1.4510
24 L C -1.2650
25 Q C -1.6306
26 L C -1.2948
27 L C 0.0000
28 K C -2.3151
29 D C -2.5080
30 L C 0.0000
31 E C -3.5043
32 R C -4.2193
33 K C -4.0087
34 Y C 0.0000
35 E C -4.4251
36 D C -4.4128
37 N C -3.3755
38 Q C -3.2624
39 R C -3.8279
40 Y C -2.3471
41 L C 0.0000
42 E C -3.5152
43 D C -2.8485
44 K C -2.3496
45 A C -1.9519
46 Q C -2.4214
47 E C -2.4388
48 L C 0.0000
49 A C -1.8402
50 R C -2.7513
51 L C -1.9042
52 E C -2.2438
53 G C -2.2193
54 E C -2.6556
55 V C 0.0000
56 R C -2.7978
57 S C -2.2328
58 L C 0.0000
59 L C -2.5388
60 K C -3.1106
61 D C -2.8152
62 I C 0.0000
63 S C -2.1530
64 Q C -2.1085
65 K C -1.5807
66 V C 0.0000
67 A C -0.5524
68 V C -0.0556
69 Y C -0.6186
70 S C -0.8456
71 T C -0.5602
72 C C -0.8932
73 R C -2.0650
1 D D -2.4902
2 T D -2.0202
3 K D -2.8534
4 D D -2.4378
5 L D -1.9349
6 N D -3.1591
7 K D -2.8468
8 L D 0.0000
9 N D -3.1094
10 E D -3.3769
11 I D 0.0000
12 E D -2.4636
13 G D -2.3198
14 T D -2.1613
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 -3.6200
29 R D -3.8630
30 K D -3.4403
31 V D 0.0000
32 S D -3.1804
33 D D -4.2312
34 L D 0.0000
35 E D -3.5915
36 N D -4.0591
37 E D -4.0656
38 A D 0.0000
39 K D -4.2887
40 K D -3.8249
41 Q D -3.0681
42 E D -2.9958
43 A D -1.9832
44 A D -1.7655
45 I D 0.0000
46 M D -1.1869
47 D D -2.5595
48 Y D 0.0000
49 N D -2.1184
50 R D -3.4219
51 D D -3.0914
52 I D 0.0000
53 E D -3.2621
54 E D -3.3949
55 I D 0.0000
56 M D -2.1266
57 K D -2.9138
58 C D -2.4529
59 I D 0.0000
60 R D -3.4638
61 N D -3.0424
62 L D 0.0000
63 E D -3.4162
64 D D -3.4986
65 I D -2.3361
66 R D -2.6464
67 K D -2.6917
68 T D -1.2446
69 L D -0.8039
70 P D -0.3015
71 S D -0.5175
72 G D -0.4612
73 C D -0.8806
74 H D -1.6863
75 N D -2.1327
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 -1.8153 1.5667 View CSV PDB
4.5 -1.9342 1.3794 View CSV PDB
5.0 -2.0807 1.3591 View CSV PDB
5.5 -2.2261 1.4067 View CSV PDB
6.0 -2.3401 1.4622 View CSV PDB
6.5 -2.4018 1.504 View CSV PDB
7.0 -2.4094 1.5255 View CSV PDB
7.5 -2.3788 1.5339 View CSV PDB
8.0 -2.3268 1.5369 View CSV PDB
8.5 -2.2595 1.5378 View CSV PDB
9.0 -2.1758 1.6835 View CSV PDB