Project name: native [mutate: YT51A, LS88A, VD89A]

Status: done

Started: 2026-08-09 08:33:17
Chain sequence(s) A: GYSEKICQIDRLIHVSSWLRNHSQFQGYVGQRGGRSQVSYYPAENSYSRWSGLLSPCDADWLGMLVVKKAKGSDMIVPGPSYKGKVFFERPTFDGYVGWGCSSGKSRTESGELCSSDSGTSSGLLPSDRVLWIGDVACQPMTPI
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
Mutated residues YT51A,LS88A,VD89A
Energy difference between WT (input) and mutated protein (by FoldX) 1.43103 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 A chain(s) selected             (00:00:00)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:00)
[INFO]       PDB-Info: The input structure is globular. Max score is recommended for pH analysis.  (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       FoldX:    Building mutant model                                                       (00:00:39)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:51)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/1a86e67f0c00dff/tmp/folded.pdb                (00:00:51)
[INFO]       Main:     Simulation completed successfully.                                          (00:01:22)
Show buried residues
Minimal score value
-3.1555
Maximal score value
1.9877
Average score
-0.7371
Total score value
-106.1376
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
24 G A -0.6271
25 Y A 0.3463
26 S A -0.6528
27 E A -1.8699
28 K A -1.2965
29 I A -0.7362
30 C A -0.8974
31 Q A -1.7249
32 I A 0.0000
33 D A -1.8889
34 R A -2.6988
35 L A 0.0000
36 I A -0.4839
37 H A 0.0000
38 V A 0.0000
39 S A 0.0000
40 S A -0.9669
41 W A -1.1976
42 L A 0.0000
43 R A -3.1555
44 N A -2.7023
45 H A -2.1360
46 S A -1.9972
47 Q A -2.7159
48 F A 0.0000
49 Q A -2.1448
50 G A -1.0595
51 T A -0.2947 mutated: YT51A
52 V A 0.0000
53 G A 0.0000
54 Q A -1.5136
55 R A -2.3575
56 G A -2.3353
57 G A -2.1387
58 R A -1.6578
59 S A -1.5611
60 Q A -2.2259
61 V A 0.0000
62 S A -0.5559
63 Y A -0.0294
64 Y A 0.5226
65 P A -0.3450
66 A A -0.6971
67 E A -1.9412
68 N A -1.4250
69 S A -0.7683
70 Y A -0.0487
71 S A -0.9484
72 R A -1.5888
73 W A 0.0468
74 S A -0.3383
75 G A -0.2803
76 L A 0.1746
77 L A 0.1796
78 S A 0.0000
79 P A 0.0000
80 C A 0.0000
81 D A 0.0000
82 A A 0.0000
83 D A -1.4226
84 W A -0.4794
85 L A -0.0802
86 G A -0.8021
87 M A -0.8901
88 S A -1.2999 mutated: LS88A
89 D A -2.4768 mutated: VD89A
90 V A -1.7210
91 K A -2.7357
92 K A -2.7382
93 A A -1.9062
94 K A -2.4956
95 G A -1.3173
96 S A -0.8730
97 D A -0.7554
98 M A 0.3360
99 I A 0.3182
100 V A 0.1802
101 P A -0.0242
102 G A -0.0230
103 P A -0.4738
104 S A -1.4427
105 Y A 0.0000
106 K A -2.6870
107 G A -1.9429
108 K A -1.5431
109 V A 0.0000
110 F A 0.0000
111 F A 0.0000
112 E A 0.0000
113 R A -0.0288
114 P A -0.0090
115 T A 0.2948
116 F A 1.0608
117 D A -0.9805
118 G A -0.8117
119 Y A -0.7603
120 V A 0.0000
121 G A 0.0000
122 W A -0.6946
123 G A -0.2753
124 C A 0.0000
125 S A -1.3654
126 S A -1.4128
127 G A -1.3555
128 K A -1.3360
129 S A 0.0000
130 R A 0.0000
131 T A -1.8607
132 E A -2.8069
133 S A -1.6838
134 G A 0.0000
135 E A -1.1177
136 L A 0.3245
137 C A -0.4595
138 S A -0.6822
139 S A -1.1041
140 D A -1.3170
141 S A -1.0441
142 G A -0.9424
143 T A 0.0000
144 S A -0.7290
145 S A -0.2110
146 G A -0.2112
147 L A 0.3534
148 L A 0.0000
149 P A -1.3852
150 S A 0.0000
151 D A -2.2553
152 R A -1.4954
153 V A 0.0000
154 L A 0.0000
155 W A 0.0000
156 I A 0.0000
157 G A -0.3533
158 D A -0.6224
159 V A 0.0983
160 A A 0.1319
161 C A -0.2535
162 Q A -0.9087
163 P A -0.3235
164 M A 0.7688
165 T A 0.7382
166 P A 0.9298
167 I A 1.9877
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 globular. Max score is recommended for pH analysis.

pH
Average A4D Score
Max A4D Score
4.0 -0.5827 4.6375 View CSV PDB
4.5 -0.6449 4.593 View CSV PDB
5.0 -0.7187 4.4975 View CSV PDB
5.5 -0.7926 4.3457 View CSV PDB
6.0 -0.8536 4.1576 View CSV PDB
6.5 -0.8913 3.9536 View CSV PDB
7.0 -0.9057 3.9417 View CSV PDB
7.5 -0.9051 3.9417 View CSV PDB
8.0 -0.8957 3.9417 View CSV PDB
8.5 -0.8783 3.9417 View CSV PDB
9.0 -0.8514 3.9417 View CSV PDB