Project name: TIMP3_5

Status: done

Started: 2026-05-22 05:07:51
Chain sequence(s) A: MTPWLGLIVLLGSWSLGDWGAEACTCSPSHPQDAFCNSDIVIRAKVVGKKLVKEGPFGTLVYTIKQMKMYRGFTKMPHVQYIHTEASESLCGLKLEVNKYQYLLTGRVYDGKMYTGLCNFVERWDQLTLSQRKGLNYRYHLGCNCKIKSCYYLPCFVTSKNECLWTDMLSNFGYPGYQSKHYACIRQKGGYCSWYRGWAPPDKSIINATDP
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]                                                (00:00:01)
[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 A chain(s) selected             (00:00:01)
[INFO]       runJob:   Creating pdb object from: input.pdb                                         (00:00:01)
[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]       Analysis: Starting Aggrescan4D on folded.pdb                                          (00:03:01)
[INFO]       agg3D:    Running pKa-ANI on                                                          
                       /STORAGE/DATA/lcbio/aggreskan/9faf08069437703/tmp/folded.pdb                (00:03:01)
[INFO]       Main:     Simulation completed successfully.                                          (00:04:44)
Show buried residues
Minimal score value
-2.2137
Maximal score value
2.6188
Average score
-0.1035
Total score value
-21.8294
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 1.0407
2 T A 0.0723
3 P A -0.0514
4 W A 1.4248
5 L A 1.6805
6 G A 0.0995
7 L A 1.8278
8 I A 2.6188
9 V A 2.4278
10 L A 2.1591
11 L A 1.7452
12 G A -0.2181
13 S A -0.0787
14 W A 1.1073
15 S A 0.3000
16 L A 1.4208
17 G A -0.5111
18 D A -1.7014
19 W A 0.7639
20 G A -0.4198
21 A A -0.3613
22 E A -1.7983
23 A A -0.2609
24 C A 0.1517
25 T A 0.0078
26 C A 0.2324
27 S A -0.1735
28 P A -0.1303
29 S A -0.1061
30 H A 0.0000
31 P A 0.0000
32 Q A 0.0000
33 D A -0.5463
34 A A -0.0950
35 F A 0.0000
36 C A -0.1906
37 N A -1.2561
38 S A 0.0000
39 D A -0.3366
40 I A 0.0000
41 V A 0.0000
42 I A 0.0000
43 R A -0.4588
44 A A 0.0000
45 K A -0.6205
46 V A 0.0000
47 V A 0.3409
48 G A -0.3309
49 K A -2.0250
50 K A -1.8867
51 L A 0.4338
52 V A 0.2400
53 K A -1.9541
54 E A -2.2137
55 G A -0.8397
56 P A 0.0087
57 F A 1.8954
58 G A 0.0000
59 T A -0.0903
60 L A 0.0000
61 V A 0.1700
62 Y A 0.0000
63 T A 0.0775
64 I A 0.0000
65 K A -1.7561
66 Q A -0.5202
67 M A 0.2583
68 K A -1.1397
69 M A 0.0000
70 Y A 0.0152
71 R A -0.6002
72 G A 0.1882
73 F A 1.8875
74 T A -0.0285
75 K A -1.6904
76 M A -0.2286
77 P A -0.1151
78 H A -1.0319
79 V A 0.0000
80 Q A -1.0350
81 Y A 0.6797
82 I A 0.0000
83 H A 0.0000
84 T A 0.0000
85 E A -0.7045
86 A A -0.1288
87 S A -0.3690
88 E A -1.8218
89 S A -0.2834
90 L A 0.5086
91 C A 0.1290
92 G A 0.0000
93 L A 0.0000
94 K A -1.7000
95 L A 0.0000
96 E A -0.9068
97 V A 0.3544
98 N A -1.4373
99 K A -1.8862
100 Y A -0.1325
101 Q A -0.3106
102 Y A 0.0000
103 L A 0.0000
104 L A 0.0000
105 T A 0.0000
106 G A 0.0000
107 R A -0.7827
108 V A 0.3086
109 Y A 0.9578
110 D A -1.6472
111 G A -0.9463
112 K A -0.9690
113 M A 0.0000
114 Y A 0.5069
115 T A 0.0000
116 G A 0.0000
117 L A 0.7600
118 C A 0.5925
119 N A -0.2628
120 F A 0.2104
121 V A 0.2476
122 E A -0.4637
123 R A -0.5127
124 W A -0.2813
125 D A -1.9798
126 Q A -1.5168
127 L A 0.0000
128 T A 0.0823
129 L A 0.5348
130 S A 0.0000
131 Q A 0.0000
132 R A -0.8208
133 K A -1.5915
134 G A 0.0000
135 L A 0.0000
136 N A -1.0337
137 Y A 1.0837
138 R A 0.0000
139 Y A 0.0000
140 H A -0.8985
141 L A 0.3360
142 G A 0.0000
143 C A 0.0631
144 N A -1.2076
145 C A -0.4642
146 K A -1.6493
147 I A -0.1857
148 K A -0.3749
149 S A -0.1520
150 C A 0.0000
151 Y A 1.3389
152 Y A 1.7956
153 L A 1.7159
154 P A 0.2026
155 C A 0.4507
156 F A 2.2088
157 V A 1.6559
158 T A 0.1483
159 S A -0.4222
160 K A -1.7103
161 N A -0.8228
162 E A 0.0000
163 C A 0.0000
164 L A 0.2216
165 W A 0.0000
166 T A -0.0139
167 D A 0.0000
168 M A 0.2192
169 L A 0.1948
170 S A -0.4071
171 N A -1.0550
172 F A 1.1565
173 G A 0.2019
174 Y A 1.1247
175 P A 0.1762
176 G A 0.0000
177 Y A 1.2860
178 Q A 0.1030
179 S A 0.0000
180 K A -0.6352
181 H A -0.2899
182 Y A 0.0392
183 A A 0.0000
184 C A 0.0000
185 I A -0.1009
186 R A -1.6741
187 Q A -0.9730
188 K A -1.8497
189 G A -0.8036
190 G A -0.1247
191 Y A 0.5342
192 C A 0.0000
193 S A -0.0088
194 W A 0.3412
195 Y A 0.5276
196 R A -1.0956
197 G A -0.0772
198 W A 1.1772
199 A A 0.2111
200 P A -0.2141
201 P A -0.5904
202 D A -2.1374
203 K A -2.0616
204 S A -0.1438
205 I A 2.3446
206 I A 2.1414
207 N A -0.8674
208 A A -0.1748
209 T A -0.3995
210 D A -1.8433
211 P A -0.5792
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 0.0431 4.5143 View CSV PDB
4.5 0.0236 4.5143 View CSV PDB
5.0 0.0019 4.5143 View CSV PDB
5.5 -0.0163 4.5143 View CSV PDB
6.0 -0.0249 4.5143 View CSV PDB
6.5 -0.0195 4.5143 View CSV PDB
7.0 -0.002 4.5143 View CSV PDB
7.5 0.0226 4.5143 View CSV PDB
8.0 0.0506 4.5143 View CSV PDB
8.5 0.0813 4.5143 View CSV PDB
9.0 0.1153 4.5143 View CSV PDB