Project name: GAVR

Status: done

Started: 2026-06-26 13:22:42
Chain sequence(s) A: MRFPSIFTAVLFAASSALAAPVNTTTEDETAQIPAEAVIGYSDLEGDFDVAVLPFSNSTNNGLLFINTTIASIAAKEEGVSLEKRGAVRFVNQLGSLVEALYLVGERGFFYTDKTRDADDRGIVEQTSISLYQLENYN
input PDB
Selected Chain(s) A
Distance of aggregation 5 Å
FoldX usage Yes
pH calculations Yes
alphaCutter usage No
Dynamic mode No
Automated mutations No
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 partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:01)
[INFO]       FoldX:    Starting FoldX energy minimization                                          (00:00:01)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:01:20)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/c56f5f2ded81b3c/tmp/folded.pdb                (00:01:20)
[INFO]       Main:     Simulation completed successfully.                                          (00:02:13)
Show buried residues
Minimal score value
-2.3549
Maximal score value
2.053
Average score
-0.1487
Total score value
-20.5217
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 M A 0.7225
2 R A -1.6154
3 F A -0.0917
4 P A -0.0275
5 S A 0.1439
6 I A 2.0168
7 F A 0.6001
8 T A 0.0300
9 A A 0.3193
10 V A 1.8760
11 L A 1.2277
12 F A 2.0530
13 A A 0.4229
14 A A 0.0244
15 S A -0.2430
16 S A -0.2485
17 A A 0.2529
18 L A 1.5541
19 A A 0.3014
20 A A 0.0388
21 P A 0.1365
22 V A 0.9360
23 N A -1.0696
24 T A -0.2746
25 T A -0.0294
26 T A 0.0000
27 E A -2.1444
28 D A -2.2745
29 E A -1.1948
30 T A -0.2125
31 A A 0.0437
32 Q A 0.0000
33 I A 0.2626
34 P A 0.0153
35 A A -0.3203
36 E A -1.7244
37 A A -0.1928
38 V A 0.6016
39 I A 0.6286
40 G A -0.1885
41 Y A 0.2656
42 S A 0.0000
43 D A -0.9051
44 L A 0.9624
45 E A -1.5618
46 G A -0.8021
47 D A -1.5561
48 F A 0.9038
49 D A -1.4207
50 V A 0.0031
51 A A 0.2561
52 V A 1.2828
53 L A 0.5505
54 P A -0.1407
55 F A 0.0000
56 S A -0.2482
57 N A -0.4290
58 S A -0.2474
59 T A -0.3406
60 N A -1.5189
61 N A -1.5469
62 G A -0.3612
63 L A 0.2777
64 L A 0.5359
65 F A 1.7883
66 I A 0.2758
67 N A -1.1764
68 T A -0.2956
69 T A -0.0105
70 I A 0.4088
71 A A 0.0448
72 S A -0.0712
73 I A 0.7558
74 A A 0.1584
75 A A -0.2390
76 K A -1.8808
77 E A -1.7558
78 E A -2.1124
79 G A -0.6125
80 V A 0.8408
81 S A 0.1607
82 L A 1.1493
83 E A -0.8548
84 K A -2.0652
85 R A -1.5707
86 G A -0.6767
87 A A 0.2476
88 V A 1.5571
89 R A -0.7002
90 F A 1.0574
91 V A 1.0033
92 N A -0.2399
93 Q A -1.2302
95 L A 1.5477
97 G A -0.1304
98 S A -0.2292
100 L A 0.0000
101 V A 0.5402
102 E A -1.6721
103 A A 0.0000
104 L A 0.0000
105 Y A 1.5457
106 L A 1.8410
107 V A 0.6033
109 G A -0.3164
110 E A -2.1927
111 R A -2.2552
112 G A -0.6812
113 F A 0.9796
114 F A 2.0263
115 Y A 0.7919
116 T A -0.1940
117 D A -1.3002
118 K A -0.9916
119 T A 0.0000
120 R A -1.1827
121 D A -1.2845
122 A A -0.4596
123 D A -2.1045
124 D A -2.3549
125 R A -1.6790
126 G A 0.0000
127 I A 0.1495
128 V A 0.0000
129 E A -0.3756
130 Q A -0.6386
133 T A -0.0304
134 S A 0.2134
135 I A 0.4012
137 S A -0.0948
138 L A 0.8549
139 Y A 1.2317
140 Q A -0.8669
141 L A 0.0000
142 E A -0.8540
143 N A -1.0289
144 Y A 0.4729
146 N A -1.0752
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 0.152 4.4805 View CSV PDB
4.5 0.1097 4.4805 View CSV PDB
5.0 0.0556 4.4805 View CSV PDB
5.5 -0.0025 4.4805 View CSV PDB
6.0 -0.0569 4.4805 View CSV PDB
6.5 -0.1011 4.4805 View CSV PDB
7.0 -0.1331 4.4805 View CSV PDB
7.5 -0.1558 4.4805 View CSV PDB
8.0 -0.1729 4.4805 View CSV PDB
8.5 -0.1854 4.4805 View CSV PDB
9.0 -0.1924 4.4804 View CSV PDB