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] [mutate: HK74D]

Status: done

Started: 2025-04-25 19:51:18
Chain sequence(s) C: DARRKAEMLQNEAKTLLAQANSKLQLLKDLERKYEDNQRYLEDKAQELARLEGEVRSLLKDISQKVAVYSTCR
B: ENVERWQGQYEGLRGQDLGQAVLDAGHSVSTLEKTLPQLLAKLSILENRGVHNASSALSASIGRVRELCAQARGAASKVKV
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 HK74D
Energy difference between WT (input) and mutated protein (by FoldX) -0.320042 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                                                       (00:01:46)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:59)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c713b5b2dee2205/tmp/folded.pdb                (00:01:59)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:08)
Show buried residues
Minimal score value
-4.4506
Maximal score value
0.8176
Average score
-1.6899
Total score value
-398.8087
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 -2.3625
34 K B -2.3970
35 T B -1.5437
36 L B 0.0000
37 P B -1.3481
38 Q B -1.4786
39 L B 0.0000
40 L B -0.0620
41 A B -0.0207
42 K B -0.3810
43 L B 0.0000
44 S B -0.2573
45 I B 0.7353
46 L B 0.0000
47 E B -2.0925
48 N B -1.4722
49 R B -0.8564
50 G B -0.4122
51 V B 0.8176
52 H B -0.3892
53 N B -1.2676
54 A B 0.0000
55 S B -0.7056
56 S B -0.4823
57 A B -0.6649
58 L B 0.0000
59 S B -0.4639
60 A B -0.4971
61 S B -0.9645
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 -2.2332
79 V B 0.0000
80 K B -1.2777
81 V B 0.6621
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 -1.4218
22 S C -1.1838
23 K C -1.4507
24 L C -1.2882
25 Q C -1.6312
26 L C -1.2983
27 L C 0.0000
28 K C -2.3363
29 D C -2.5229
30 L C 0.0000
31 E C -2.9321
32 R C -4.2164
33 K C -4.0837
34 Y C 0.0000
35 E C -4.4239
36 D C -4.4506
37 N C -3.4382
38 Q C -3.2739
39 R C -3.8925
40 Y C -2.4101
41 L C 0.0000
42 E C -3.6321
43 D C -2.9475
44 K C -2.3622
45 A C -2.1745
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 -2.1522
64 Q C -2.1071
65 K C -1.5772
66 V C 0.0000
67 A C -0.5487
68 V C -0.1328
69 Y C -0.7861
70 S C -0.9658
71 T C -0.6489
72 C C -1.0422
73 R C -2.1751
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 -3.4423
31 V D 0.0000
32 S D -3.1814
33 D D -4.2305
34 L D 0.0000
35 E D -3.5958
36 N D -4.0683
37 E D -4.0617
38 A D 0.0000
39 K D -4.3103
40 K D -3.8430
41 Q D -3.0724
42 E D -3.0560
43 A D -1.9888
44 A D -1.6941
45 I D 0.0000
46 M D -1.1456
47 D D -2.4798
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 -2.6484
67 K D -2.6940
68 T D -1.2484
69 L D -0.8067
70 P D -0.4071
71 S D -0.6026
72 G D -0.6543
73 C D -1.2905
74 K D -2.4263 mutated: HK74D
75 N D -2.4991
76 T D -1.2003
77 P D -0.8272
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 -1.7744 1.7 View CSV PDB
4.5 -1.8945 1.6359 View CSV PDB
5.0 -2.0436 1.5334 View CSV PDB
5.5 -2.1933 1.4081 View CSV PDB
6.0 -2.313 1.2822 View CSV PDB
6.5 -2.3806 1.1791 View CSV PDB
7.0 -2.3929 1.1196 View CSV PDB
7.5 -2.3649 1.2392 View CSV PDB
8.0 -2.314 1.3875 View CSV PDB
8.5 -2.2474 1.5384 View CSV PDB
9.0 -2.164 1.6864 View CSV PDB