Project name: Test_RNF5

Status: done

Started: 2026-02-04 11:53:13
Chain sequence(s) A: MAAAEEEDGGPEGPNRERGGAGATFECNICLETAREAVVSVCGHLYCWPCLHQWLETRPERQECPVCKAGISREKVVPLYGRGSQKPQDPRLKTPPRPQGQRPAPESRGGFQPFGDTGGFHFSFGVGAFPFGFFTTVFNAHEPFRRGTGVDLGQGHPASSWQDSLFLFLAIFFFFWLLSI
input PDB
Selected Chain(s) A
Distance of aggregation 10 Å
FoldX usage No
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]                                                (00:00:12)
[WARNING]    runJob:   Working directory already exists (possibly overwriting previous results -ow 
                       to prevent this behavior)                                                   (00:00:12)
[INFO]       runJob:   Starting aggrescan3d job on: input.pdb with A chain(s) selected             (00:00:12)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:12)
[INFO]       PDB-Info: The input structure is partially or entirely disordered. Average score is   
                       recommended for pH analysis.                                                (00:00:13)
[INFO]       runJob:   FoldX not utilized. Treating input pdb file as it was already optimized.    (00:00:13)
[INFO]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:00:13)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/2698b664bd0746a/tmp/folded.pdb                (00:00:13)
[INFO]       Main:     Simulation completed successfully.                                          (00:03:26)
Show buried residues
Minimal score value
-4.311
Maximal score value
6.6492
Average score
-0.2278
Total score value
-40.9968
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 1.1041
2 A A 0.3883
3 A A -0.3409
4 A A -1.3885
5 E A -3.3627
6 E A -4.1007
7 E A -4.2445
8 D A -3.7833
9 G A -2.6622
10 G A -2.0917
11 P A -1.8750
12 E A -2.6389
13 G A -2.2258
14 P A -2.4048
15 N A -3.5923
16 R A -4.1426
17 E A -4.3110
18 R A -3.8589
19 G A -2.6031
20 G A -1.7052
21 A A -0.8774
22 G A -0.3900
23 A A 0.0295
24 T A -0.0430
25 F A 0.6120
26 E A -1.2790
27 C A 0.0000
28 N A -0.0189
29 I A 0.6578
30 C A 0.3326
31 L A 0.4801
32 E A -1.5455
33 T A -1.2363
34 A A -1.0634
35 R A -2.5508
36 E A -1.5114
37 A A 0.0037
38 V A 0.0000
39 V A 1.1441
40 S A 0.0000
41 V A 1.4488
42 C A 0.6658
43 G A 0.4806
44 H A 0.0737
45 L A 0.0000
46 Y A 0.0000
47 C A 0.0000
48 W A 0.0000
49 P A -0.6950
50 C A -0.3414
51 L A 0.0000
52 H A -1.3186
53 Q A -1.9353
54 W A -1.5962
55 L A -2.6276
56 E A -3.1890
57 T A -2.4448
58 R A -3.6584
59 P A -3.1509
60 E A -3.7433
61 R A -4.2695
62 Q A -3.5511
63 E A -2.6866
64 C A 0.0000
65 P A -0.0861
66 V A 0.8728
67 C A 0.0187
68 K A -1.8218
69 A A -0.7513
70 G A -1.5640
71 I A 0.0000
72 S A -2.0501
73 R A -2.3219
74 E A -2.7038
75 K A -1.7315
76 V A 0.0000
77 V A 1.2034
78 P A 0.0000
79 L A 1.0451
80 Y A 0.9343
81 G A -0.9063
82 R A -2.1990
83 G A -2.3042
84 S A -2.1978
85 Q A -2.9664
86 K A -3.1864
87 P A -2.1103
88 Q A -2.5470
89 D A -2.3467
90 P A -1.8325
91 R A -2.2064
92 L A -0.7861
93 K A -1.8301
94 T A -1.1868
95 P A -0.5426
96 P A -0.8971
97 R A -0.8231
98 P A -1.4582
99 Q A -1.7832
100 G A -1.1797
101 Q A -2.2769
102 R A -2.7803
103 P A -1.8149
104 A A -1.3075
105 P A -1.7945
106 E A -2.6774
107 S A -2.3321
108 R A -2.6013
109 G A -1.6832
110 G A -0.7216
111 F A 0.9700
112 Q A -0.1401
113 P A 0.2334
114 F A 1.3089
115 G A -0.7280
116 D A -1.8280
117 T A -0.9162
118 G A -0.6452
119 G A 0.1459
120 F A 1.8888
121 H A 1.2935
122 F A 2.8908
123 S A 2.3216
124 F A 3.0523
125 G A 2.0317
126 V A 2.5910
127 G A 1.5099
128 A A 2.5672
129 F A 3.9764
130 P A 2.9719
131 F A 3.8115
132 G A 2.6780
133 F A 4.2095
134 F A 4.5077
135 T A 2.5050
136 T A 2.1283
137 V A 3.2275
138 F A 2.4327
139 N A -0.0111
140 A A -0.0486
141 H A -1.4769
142 E A -2.2437
143 P A -1.4427
144 F A -0.5594
145 R A -2.3010
146 R A -2.2995
147 G A -1.5421
148 T A -1.1523
149 G A -0.2946
150 V A 0.8084
151 D A -0.6085
152 L A 0.6038
153 G A -0.8402
154 Q A -1.8911
155 G A -1.4333
156 H A -1.7398
157 P A -1.0743
158 A A -0.7804
159 S A -0.6223
160 S A -0.4283
161 W A 0.8151
162 Q A 0.0317
163 D A -0.1512
164 S A 1.5119
165 L A 3.0949
166 F A 4.0469
167 L A 4.3435
168 F A 5.2321
169 L A 5.5047
170 A A 5.1478
171 I A 5.9966
172 F A 6.6492
173 F A 6.4200
174 F A 6.2785
175 F A 6.2002
176 W A 5.6545
177 L A 5.4106
178 L A 4.5846
179 S A 3.1348
180 I A 3.3489
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 1.1551 13.4553 View CSV PDB
4.5 1.071 13.4553 View CSV PDB
5.0 0.9648 13.4553 View CSV PDB
5.5 0.8564 13.4553 View CSV PDB
6.0 0.7654 13.4553 View CSV PDB
6.5 0.7047 13.4553 View CSV PDB
7.0 0.675 13.4553 View CSV PDB
7.5 0.6658 13.4553 View CSV PDB
8.0 0.6671 13.4553 View CSV PDB
8.5 0.675 13.4553 View CSV PDB
9.0 0.6898 13.4553 View CSV PDB