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] [mutate: KI45B, HT55B] [mutate: TS55B, LS56B]

Status: done

Started: 2025-04-25 14:45:31
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNATLALSASIGRVRELCAQARGAASKVKV
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 LS56B,TS55B
Energy difference between WT (input) and mutated protein (by FoldX) 0.307243 kcal/mol
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                                                       (00:01:50)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:54)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/61bc3999e89a5a1/tmp/folded.pdb                (00:01:54)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:05)
Show buried residues
Minimal score value
-4.4511
Maximal score value
0.8161
Average score
-1.6775
Total score value
-395.8807
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 -2.3630
34 K B -2.3979
35 T B -1.5452
36 L B 0.0000
37 P B -1.3503
38 Q B -1.4830
39 L B 0.0000
40 L B -0.0607
41 A B -0.0171
42 K B -0.3749
43 L B 0.0000
44 S B -0.2481
45 I B 0.7556
46 L B 0.0000
47 E B -2.0867
48 N B -1.4664
49 R B -0.8532
50 G B -0.4118
51 V B 0.8161
52 H B -0.3917
53 N B -1.2684
54 A B 0.0000
55 S B -0.7057 mutated: TS55B
56 S B -0.4827 mutated: LS56B
57 A B -0.6651
58 L B 0.0000
59 S B -0.4639
60 A B -0.4971
61 S B -0.9644
62 I B 0.0000
63 G B -1.8939
64 R B -2.3881
65 V B 0.0000
66 R B -2.8704
67 E B -3.2650
68 L B 0.0000
69 C B 0.0000
70 A B -2.0122
71 Q B -2.3067
72 A B 0.0000
73 R B -2.3711
74 G B -1.6876
75 A B -1.7731
76 A B -1.4650
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 -0.9501
19 Q C -1.2557
20 A C 0.0000
21 N C -1.4223
22 S C -1.1838
23 K C -1.4507
24 L C -1.2890
25 Q C -1.6309
26 L C -1.2979
27 L C 0.0000
28 K C -2.3361
29 D C -2.5235
30 L C 0.0000
31 E C -2.9287
32 R C -4.2174
33 K C -4.0879
34 Y C 0.0000
35 E C -4.4238
36 D C -4.4511
37 N C -3.4383
38 Q C -3.2723
39 R C -3.8915
40 Y C -2.4091
41 L C 0.0000
42 E C -3.6316
43 D C -2.9471
44 K C -2.3618
45 A C -2.1744
46 Q C -2.5560
47 E C -2.5062
48 L C 0.0000
49 A C -1.8760
50 R C -2.7768
51 L C -1.9233
52 E C -2.2738
53 G C -2.2312
54 E C -2.6667
55 V C 0.0000
56 R C -2.8311
57 S C -2.2496
58 L C 0.0000
59 L C -2.5516
60 K C -3.1199
61 D C -2.8202
62 I C 0.0000
63 S C -2.1533
64 Q C -2.1087
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 -3.6199
29 R D -3.8634
30 K D -3.4413
31 V D 0.0000
32 S D -3.1820
33 D D -4.2329
34 L D 0.0000
35 E D -3.5982
36 N D -4.0695
37 E D -4.0786
38 A D 0.0000
39 K D -4.3143
40 K D -3.8486
41 Q D -3.0778
42 E D -3.0591
43 A D -1.9913
44 A D -1.6944
45 I D 0.0000
46 M D -1.1457
47 D D -2.4799
48 Y D -1.8826
49 N D -2.0328
50 R D -3.3688
51 D D -3.0389
52 I D 0.0000
53 E D -3.2508
54 E D -3.4168
55 I D 0.0000
56 M D -2.1362
57 K D -2.9240
58 C D -2.4676
59 I D 0.0000
60 R D -3.4665
61 N D -3.0412
62 L D 0.0000
63 E D -3.4158
64 D D -3.4983
65 I D -2.3361
66 R D -2.6465
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
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 -1.7654 1.7286 View CSV PDB
4.5 -1.8856 1.665 View CSV PDB
5.0 -2.0346 1.5629 View CSV PDB
5.5 -2.1839 1.4378 View CSV PDB
6.0 -2.3032 1.3122 View CSV PDB
6.5 -2.3716 1.2096 View CSV PDB
7.0 -2.3871 1.1505 View CSV PDB
7.5 -2.3645 1.2358 View CSV PDB
8.0 -2.3201 1.3843 View CSV PDB
8.5 -2.2599 1.5354 View CSV PDB
9.0 -2.183 1.6835 View CSV PDB