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

Status: done

Started: 2025-04-25 14:14:18
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNASSALSASIGRVRELCAQARGAASKVKV
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 NA53B,SL56B
Energy difference between WT (input) and mutated protein (by FoldX) 1.00904 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                                                       (00:01:44)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:48)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/417d6741d9281b3/tmp/folded.pdb                (00:01:48)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:57)
Show buried residues
Minimal score value
-4.4299
Maximal score value
1.6785
Average score
-1.6753
Total score value
-395.3685
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 -2.3281
18 L B -2.3802
19 G B -1.7883
20 Q B -1.7582
21 A B 0.0000
22 V B 0.0000
23 L B -0.0158
24 D B -1.1114
25 A B 0.0000
26 G B -1.0074
27 H B -1.2943
28 S B -1.4221
29 V B 0.0000
30 S B -1.3323
31 T B -1.4045
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 -1.6788
43 L B 0.0000
44 S B -2.0420
45 K B -2.9683
46 L B 0.0000
47 E B -3.2585
48 N B -2.6697
49 R B -1.8688
50 G B -0.6796
51 V B 1.2708
52 H B 0.3936
53 A B 0.6562 mutated: NA53B
54 A B -0.0830
55 S B 0.6862
56 L B 1.6785 mutated: SL56B
57 A B 0.6258
58 L B 0.0000
59 S B 0.1357
60 A B -0.0387
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 -2.7949
67 E B -3.2217
68 L B 0.0000
69 C B 0.0000
70 A B -1.9826
71 Q B -2.2693
72 A B 0.0000
73 R B -2.3642
74 G B -1.6791
75 A B -1.7674
76 A B -1.4622
77 S B -1.6463
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 -2.2973
3 R C -3.3122
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 -2.1552
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 -1.4507
24 L C -1.2645
25 Q C -1.6290
26 L C -1.2926
27 L C 0.0000
28 K C -2.3195
29 D C -2.5185
30 L C 0.0000
31 E C -3.5169
32 R C -4.2408
33 K C -4.0726
34 Y C 0.0000
35 E C -4.4299
36 D C -4.3512
37 N C -3.3178
38 Q C -2.9095
39 R C -3.5813
40 Y C -2.1179
41 L C 0.0000
42 E C -2.6329
43 D C -2.5295
44 K C -2.0771
45 A C -1.6510
46 Q C -2.2634
47 E C -2.3613
48 L C 0.0000
49 A C -1.8462
50 R C -2.7553
51 L C -1.9052
52 E C -2.2420
53 G C -2.2169
54 E C -2.6531
55 V C 0.0000
56 R C -2.7890
57 S C -2.2295
58 L C 0.0000
59 L C -2.5380
60 K C -3.1118
61 D C -2.8157
62 I C 0.0000
63 S C -2.1521
64 Q C -2.1097
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 -2.4894
2 T D -2.0199
3 K D -2.8532
4 D D -2.4382
5 L D -1.9351
6 N D -3.1605
7 K D -2.8526
8 L D 0.0000
9 N D -3.1106
10 E D -3.3786
11 I D 0.0000
12 E D -2.4646
13 G D -2.3203
14 T D -2.1616
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 -3.4415
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 -3.1799
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 -2.9264
58 C D -2.4573
59 I D 0.0000
60 R D -3.4668
61 N D -3.0443
62 L D 0.0000
63 E D -3.4143
64 D D -3.4966
65 I D -2.3349
66 R D -2.6460
67 K D -2.6907
68 T D -1.2441
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 -1.7873 2.1815 View CSV PDB
4.5 -1.9057 2.1833 View CSV PDB
5.0 -2.0521 2.1883 View CSV PDB
5.5 -2.1982 2.1989 View CSV PDB
6.0 -2.3136 2.2142 View CSV PDB
6.5 -2.3769 2.2282 View CSV PDB
7.0 -2.3863 2.2364 View CSV PDB
7.5 -2.3571 2.2399 View CSV PDB
8.0 -2.3061 2.2412 View CSV PDB
8.5 -2.2394 2.2416 View CSV PDB
9.0 -2.1558 2.2417 View CSV PDB