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]

Status: done

Started: 2025-04-25 14:30:07
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSKLENRGVHNAKLALSASIGRVRELCAQARGAASKVKV
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 KR55B
Energy difference between WT (input) and mutated protein (by FoldX) -0.507634 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                                                       (00:01:53)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:02:06)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/9592870fac52abf/tmp/folded.pdb                (00:02:06)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:13)
Show buried residues
Minimal score value
-4.4444
Maximal score value
0.8806
Average score
-1.6847
Total score value
-397.5921
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 -1.7845
20 Q B -1.7536
21 A B 0.0000
22 V B 0.0000
23 L B -0.0010
24 D B -1.1043
25 A B 0.0000
26 G B -0.9995
27 H B -1.2900
28 S B -1.4197
29 V B 0.0000
30 S B -1.3318
31 T B -1.4043
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 -1.6792
43 L B 0.0000
44 S B -2.0652
45 K B -3.0117
46 L B 0.0000
47 E B -3.3098
48 N B -2.7519
49 R B -1.9953
50 G B -0.8740
51 V B 0.8806
52 H B -0.1943
53 N B -0.8177
54 A B 0.0000
55 R B -0.4444 mutated: KR55B
56 L B 0.8792
57 A B 0.0504
58 L B 0.0000
59 S B -0.1001
60 A B -0.1615
61 S B -0.7889
62 I B 0.0000
63 G B -1.8741
64 R B -2.3581
65 V B 0.0000
66 R B -2.7998
67 E B -3.2285
68 L B 0.0000
69 C B 0.0000
70 A B -1.9940
71 Q B -2.2939
72 A B 0.0000
73 R B -2.3713
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 -2.1534
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 -1.6302
26 L C -1.2943
27 L C 0.0000
28 K C -2.3139
29 D C -2.5069
30 L C 0.0000
31 E C -3.5187
32 R C -4.2233
33 K C -4.0002
34 Y C 0.0000
35 E C -4.4444
36 D C -4.3517
37 N C -3.2629
38 Q C -3.1713
39 R C -3.5932
40 Y C -2.1168
41 L C 0.0000
42 E C -2.8418
43 D C -2.4939
44 K C -2.1455
45 A C -1.7504
46 Q C -2.2390
47 E C -2.3453
48 L C 0.0000
49 A C -1.8441
50 R C -2.7542
51 L C -1.9065
52 E C -2.2444
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 -2.0195
3 K D -2.8521
4 D D -2.4361
5 L D -1.9334
6 N D -3.1568
7 K D -2.8421
8 L D 0.0000
9 N D -3.1078
10 E D -3.3752
11 I D 0.0000
12 E D -2.4630
13 G D -2.3193
14 T D -2.1614
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 -3.4412
31 V D 0.0000
32 S D -3.1954
33 D D -4.2578
34 L D 0.0000
35 E D -3.6097
36 N D -4.0898
37 E D -4.1177
38 A D 0.0000
39 K D -4.2714
40 K D -3.7839
41 Q D 0.0000
42 E D -2.9106
43 A D -1.9157
44 A D -1.7286
45 I D 0.0000
46 M D -1.0985
47 D D -2.4599
48 Y D -1.9916
49 N D -2.0341
50 R D -3.3691
51 D D -3.0426
52 I D 0.0000
53 E D -3.2465
54 E D -3.3907
55 I D 0.0000
56 M D -2.1357
57 K D -2.9297
58 C D -2.4598
59 I D 0.0000
60 R D -3.4689
61 N D -3.0457
62 L D 0.0000
63 E D -3.4174
64 D D -3.4985
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
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 -1.8149 1.5632 View CSV PDB
4.5 -1.9328 1.3751 View CSV PDB
5.0 -2.078 1.1793 View CSV PDB
5.5 -2.2228 1.026 View CSV PDB
6.0 -2.3374 0.9606 View CSV PDB
6.5 -2.4006 0.995 View CSV PDB
7.0 -2.4103 1.0991 View CSV PDB
7.5 -2.3821 1.2358 View CSV PDB
8.0 -2.3327 1.3843 View CSV PDB
8.5 -2.2678 1.5354 View CSV PDB
9.0 -2.1862 1.6835 View CSV PDB