| Chain sequence(s) |
A: DIVMTQTPLSLSVTPGQPASISCRSSQSLVHSNGNTYLEWYLQKPGQPPQLLIYKLSNRFSGVPDRFSGSGSGTDFTLKISRVEAEDVGVYYCFQGSQVPFTFGSGTKLEIKGGGGSGGGGSGGGGSVQLVQSGAEVKKPGASVKVSCKASGYTFTDYIMLWVRQAPGQGLEWMGNIDPYYGSTGYALKFKGRVTMTRDTSTSTVYMELSSLRSEDTAVYYCARDGNYGSDYWGQGTTVTVSS
B: AQEVQQSPHCTTVPVGASVNITCSTSGGLRGIYLRQLGPQPQDIIYYEDGVVPTTDRRFRGRIDFSGSQDNLTITMHRLQLSDTGTYTCQAITEVNVYGSGTLVLVTEEQSQGWHRCSDAPPRASALPAPPTGSALPDPQTASALPDPPAASALP input PDB |
| Selected Chain(s) | A,B |
| Distance of aggregation | 10 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] (00:00:02)
[WARNING] runJob: Working directory already exists (possibly overwriting previous results -ow
to prevent this behavior) (00:00:02)
[INFO] runJob: Starting aggrescan3d job on: input.pdb with all chain(s) selected (00:00:02)
[INFO] runJob: Creating pdb object from: input.pdb (00:00:02)
[INFO] PDB-Info: The input structure is globular. Max score is recommended for pH analysis. (00:00:04)
[INFO] FoldX: Starting FoldX energy minimization (00:00:04)
[INFO] Analysis: Starting Aggrescan4D on folded.pdb (00:05:24)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/d12b4d54b2878b8/tmp/folded.pdb (00:05:24)
[INFO] Main: Simulation completed successfully. (00:11:28)
|
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 | D | A | -1.4315 | |
| 2 | I | A | 0.0000 | |
| 3 | V | A | 0.7285 | |
| 4 | M | A | 0.0000 | |
| 5 | T | A | -0.2738 | |
| 6 | Q | A | 0.0000 | |
| 7 | T | A | 0.0460 | |
| 8 | P | A | 0.4657 | |
| 9 | L | A | 1.2670 | |
| 10 | S | A | 0.1578 | |
| 11 | L | A | -0.2248 | |
| 12 | S | A | -1.1210 | |
| 13 | V | A | 0.0000 | |
| 14 | T | A | -1.5939 | |
| 15 | P | A | -1.7320 | |
| 16 | G | A | -1.6074 | |
| 17 | Q | A | -1.8217 | |
| 18 | P | A | -1.9695 | |
| 19 | A | A | 0.0000 | |
| 20 | S | A | -0.8760 | |
| 21 | I | A | 0.0000 | |
| 22 | S | A | -0.8627 | |
| 23 | C | A | 0.0000 | |
| 24 | R | A | -2.2384 | |
| 25 | S | A | 0.0000 | |
| 26 | S | A | -1.0119 | |
| 27 | Q | A | -1.5882 | |
| 28 | S | A | -0.9000 | |
| 29 | L | A | 0.0000 | |
| 30 | V | A | 0.5784 | |
| 31 | H | A | -0.3355 | |
| 32 | S | A | -0.6494 | |
| 33 | N | A | -1.3771 | |
| 34 | G | A | -0.8627 | |
| 35 | N | A | -0.5272 | |
| 36 | T | A | -0.0198 | |
| 37 | Y | A | 0.0000 | |
| 38 | L | A | 0.0000 | |
| 39 | E | A | 0.0000 | |
| 40 | W | A | 0.0000 | |
| 41 | Y | A | 0.0000 | |
| 42 | L | A | 0.0000 | |
| 43 | Q | A | -0.8367 | |
| 44 | K | A | -1.4561 | |
| 45 | P | A | -1.0417 | |
| 46 | G | A | -1.3930 | |
| 47 | Q | A | -1.9068 | |
| 48 | P | A | -1.1747 | |
| 49 | P | A | 0.0000 | |
| 50 | Q | A | -0.8741 | |
| 51 | L | A | 0.0000 | |
| 52 | L | A | 0.0000 | |
| 53 | I | A | 0.0000 | |
| 54 | Y | A | -0.3366 | |
| 55 | K | A | -0.5818 | |
| 56 | L | A | -0.4972 | |
| 57 | S | A | -0.7698 | |
| 58 | N | A | -1.1443 | |
| 59 | R | A | -1.5882 | |
| 60 | F | A | -0.5912 | |
| 61 | S | A | -0.5759 | |
| 62 | G | A | -0.9288 | |
| 63 | V | A | -0.8827 | |
| 64 | P | A | -1.2484 | |
| 65 | D | A | -2.4022 | |
| 66 | R | A | -2.2958 | |
| 67 | F | A | 0.0000 | |
| 68 | S | A | -1.5331 | |
| 69 | G | A | 0.0000 | |
| 70 | S | A | -0.9276 | |
| 71 | G | A | -0.9737 | |
| 72 | S | A | -0.6630 | |
| 73 | G | A | -0.6128 | |
| 74 | T | A | -1.4208 | |
| 75 | D | A | -2.0640 | |
| 76 | F | A | 0.0000 | |
| 77 | T | A | -1.1279 | |
| 78 | L | A | 0.0000 | |
| 79 | K | A | -2.1896 | |
| 80 | I | A | 0.0000 | |
| 81 | S | A | -2.3374 | |
| 82 | R | A | -3.1279 | |
| 83 | V | A | 0.0000 | |
| 84 | E | A | -2.1664 | |
| 85 | A | A | -1.6782 | |
| 86 | E | A | -2.2068 | |
| 87 | D | A | 0.0000 | |
| 88 | V | A | -0.8623 | |
| 89 | G | A | 0.0000 | |
| 90 | V | A | -0.0285 | |
| 91 | Y | A | 0.0000 | |
| 92 | Y | A | 0.0000 | |
| 93 | C | A | 0.0000 | |
| 94 | F | A | 0.0000 | |
| 95 | Q | A | 0.0000 | |
| 96 | G | A | 0.0000 | |
| 97 | S | A | 0.0000 | |
| 98 | Q | A | -1.3945 | |
| 99 | V | A | -0.6890 | |
| 100 | P | A | -0.6304 | |
| 101 | F | A | 0.0000 | |
| 102 | T | A | -0.0431 | |
| 103 | F | A | 0.2926 | |
| 104 | G | A | 0.0000 | |
| 105 | S | A | -0.0317 | |
| 106 | G | A | 0.0000 | |
| 107 | T | A | 0.0000 | |
| 108 | K | A | -0.4384 | |
| 109 | L | A | 0.0000 | |
| 110 | E | A | -1.6273 | |
| 111 | I | A | -1.8269 | |
| 112 | K | A | -2.3688 | |
| 113 | G | A | -1.8315 | |
| 114 | G | A | -1.8097 | |
| 115 | G | A | -1.3543 | |
| 116 | G | A | -1.3386 | |
| 117 | S | A | -1.2222 | |
| 118 | G | A | -1.6839 | |
| 119 | G | A | -1.4980 | |
| 120 | G | A | -1.8179 | |
| 121 | G | A | -1.4350 | |
| 122 | S | A | -1.2086 | |
| 123 | G | A | -1.2584 | |
| 124 | G | A | -1.2976 | |
| 125 | G | A | -1.2481 | |
| 126 | G | A | -1.0502 | |
| 127 | S | A | -0.9007 | |
| 128 | V | A | -0.8617 | |
| 129 | Q | A | -1.4323 | |
| 130 | L | A | 0.0000 | |
| 131 | V | A | -0.0545 | |
| 132 | Q | A | 0.0000 | |
| 133 | S | A | -0.6747 | |
| 134 | G | A | -0.6708 | |
| 135 | A | A | -0.1141 | |
| 136 | E | A | -0.2669 | |
| 137 | V | A | 0.8073 | |
| 138 | K | A | -0.9666 | |
| 139 | K | A | -2.1363 | |
| 140 | P | A | -2.1554 | |
| 141 | G | A | -1.4950 | |
| 142 | A | A | -1.1859 | |
| 143 | S | A | -1.2876 | |
| 144 | V | A | 0.0000 | |
| 145 | K | A | -1.9285 | |
| 146 | V | A | 0.0000 | |
| 147 | S | A | -0.7238 | |
| 148 | C | A | 0.0000 | |
| 149 | K | A | -1.2323 | |
| 150 | A | A | 0.0000 | |
| 151 | S | A | -0.7904 | |
| 152 | G | A | -0.7767 | |
| 153 | Y | A | -0.2424 | |
| 154 | T | A | -0.1072 | |
| 155 | F | A | 0.0000 | |
| 156 | T | A | 0.0472 | |
| 157 | D | A | -0.0613 | |
| 158 | Y | A | 0.0922 | |
| 159 | I | A | 0.0000 | |
| 160 | M | A | 0.0000 | |
| 161 | L | A | 0.0000 | |
| 162 | W | A | 0.0000 | |
| 163 | V | A | 0.0000 | |
| 164 | R | A | 0.0000 | |
| 165 | Q | A | -0.6046 | |
| 166 | A | A | -1.0212 | |
| 167 | P | A | -1.0249 | |
| 168 | G | A | -1.2149 | |
| 169 | Q | A | -1.6954 | |
| 170 | G | A | -0.9810 | |
| 171 | L | A | 0.0000 | |
| 172 | E | A | -0.6414 | |
| 173 | W | A | 0.0000 | |
| 174 | M | A | 0.0000 | |
| 175 | G | A | 0.0000 | |
| 176 | N | A | 0.0000 | |
| 177 | I | A | 0.0000 | |
| 178 | D | A | 0.0000 | |
| 179 | P | A | 0.0000 | |
| 180 | Y | A | 0.3742 | |
| 181 | Y | A | 0.6326 | |
| 182 | G | A | -0.0275 | |
| 183 | S | A | 0.0000 | |
| 184 | T | A | 0.0000 | |
| 185 | G | A | 0.0000 | |
| 186 | Y | A | -0.4937 | |
| 187 | A | A | 0.0000 | |
| 188 | L | A | -0.1149 | |
| 189 | K | A | -1.5470 | |
| 190 | F | A | 0.0000 | |
| 191 | K | A | -1.9592 | |
| 192 | G | A | -1.5041 | |
| 193 | R | A | -1.4080 | |
| 194 | V | A | 0.0000 | |
| 195 | T | A | -0.8919 | |
| 196 | M | A | 0.0000 | |
| 197 | T | A | -0.6757 | |
| 198 | R | A | -1.2319 | |
| 199 | D | A | -1.3147 | |
| 200 | T | A | -0.7068 | |
| 201 | S | A | -0.5837 | |
| 202 | T | A | -0.7311 | |
| 203 | S | A | -0.8459 | |
| 204 | T | A | 0.0000 | |
| 205 | V | A | 0.0000 | |
| 206 | Y | A | -0.8707 | |
| 207 | M | A | 0.0000 | |
| 208 | E | A | -1.4702 | |
| 209 | L | A | 0.0000 | |
| 210 | S | A | -1.0592 | |
| 211 | S | A | -1.0831 | |
| 212 | L | A | 0.0000 | |
| 213 | R | A | -2.7972 | |
| 214 | S | A | -2.2656 | |
| 215 | E | A | -2.4829 | |
| 216 | D | A | 0.0000 | |
| 217 | T | A | -0.8639 | |
| 218 | A | A | 0.0000 | |
| 219 | V | A | 0.2123 | |
| 220 | Y | A | 0.0000 | |
| 221 | Y | A | 0.0000 | |
| 222 | C | A | 0.0000 | |
| 223 | A | A | 0.0000 | |
| 224 | R | A | 0.0000 | |
| 225 | D | A | 0.0000 | |
| 226 | G | A | 0.0000 | |
| 227 | N | A | -0.0974 | |
| 228 | Y | A | -0.1264 | |
| 229 | G | A | 0.0000 | |
| 230 | S | A | 0.0000 | |
| 231 | D | A | -0.1132 | |
| 232 | Y | A | -0.2310 | |
| 233 | W | A | -0.3434 | |
| 234 | G | A | 0.0000 | |
| 235 | Q | A | -1.3145 | |
| 236 | G | A | -0.5695 | |
| 237 | T | A | 0.0000 | |
| 238 | T | A | -0.0132 | |
| 239 | V | A | 0.0000 | |
| 240 | T | A | -0.3389 | |
| 241 | V | A | 0.0000 | |
| 242 | S | A | -1.0834 | |
| 243 | S | A | -0.9963 | |
| 1 | A | B | -0.3914 | |
| 2 | Q | B | -1.2344 | |
| 3 | E | B | -2.2709 | |
| 4 | V | B | 0.0000 | |
| 5 | Q | B | -1.9129 | |
| 6 | Q | B | 0.0000 | |
| 7 | S | B | -0.5033 | |
| 8 | P | B | 0.0000 | |
| 9 | H | B | 0.0000 | |
| 10 | C | B | 0.0000 | |
| 11 | T | B | 0.0000 | |
| 12 | T | B | 0.0000 | |
| 13 | V | B | 0.0000 | |
| 14 | P | B | -0.9624 | |
| 15 | V | B | -0.6107 | |
| 16 | G | B | -1.2227 | |
| 17 | A | B | 0.0000 | |
| 18 | S | B | -0.7743 | |
| 19 | V | B | 0.0000 | |
| 20 | N | B | -0.9561 | |
| 21 | I | B | 0.0000 | |
| 22 | T | B | -0.8804 | |
| 23 | C | B | 0.0000 | |
| 24 | S | B | -1.8544 | |
| 25 | T | B | -1.9248 | |
| 26 | S | B | -1.6769 | |
| 27 | G | B | -1.2746 | |
| 28 | G | B | -1.4456 | |
| 29 | L | B | -1.7582 | |
| 30 | R | B | -2.4418 | |
| 31 | G | B | 0.0000 | |
| 32 | I | B | 0.0000 | |
| 33 | Y | B | 0.1669 | |
| 34 | L | B | 0.0000 | |
| 35 | R | B | -0.6765 | |
| 36 | Q | B | -0.8990 | |
| 37 | L | B | -0.6518 | |
| 38 | G | B | -1.2529 | |
| 39 | P | B | -1.3084 | |
| 40 | Q | B | -1.6753 | |
| 41 | P | B | -1.4476 | |
| 42 | Q | B | -1.4186 | |
| 43 | D | B | -0.9511 | |
| 44 | I | B | 0.0000 | |
| 45 | I | B | 0.0000 | |
| 46 | Y | B | 0.4297 | |
| 47 | Y | B | 0.0826 | |
| 48 | E | B | -0.8709 | |
| 49 | D | B | -1.4660 | |
| 50 | G | B | -0.1538 | |
| 51 | V | B | 1.4516 | |
| 52 | V | B | 2.0199 | |
| 53 | P | B | 0.7687 | |
| 54 | T | B | 0.0236 | |
| 55 | T | B | -1.4059 | |
| 56 | D | B | 0.0000 | |
| 57 | R | B | -3.4721 | |
| 58 | R | B | -3.3835 | |
| 59 | F | B | 0.0000 | |
| 60 | R | B | -3.4709 | |
| 61 | G | B | -2.3974 | |
| 62 | R | B | -2.2891 | |
| 63 | I | B | -1.5882 | |
| 64 | D | B | -1.9650 | |
| 65 | F | B | -0.6647 | |
| 66 | S | B | -0.9039 | |
| 67 | G | B | -1.2598 | |
| 68 | S | B | -1.6037 | |
| 69 | Q | B | -1.9883 | |
| 70 | D | B | -2.6520 | |
| 71 | N | B | -2.3338 | |
| 72 | L | B | 0.0000 | |
| 73 | T | B | -1.0275 | |
| 74 | I | B | 0.0000 | |
| 75 | T | B | -0.9264 | |
| 76 | M | B | 0.0000 | |
| 77 | H | B | -1.7256 | |
| 78 | R | B | -2.2113 | |
| 79 | L | B | 0.0000 | |
| 80 | Q | B | -0.9400 | |
| 81 | L | B | 0.2212 | |
| 82 | S | B | -0.1308 | |
| 83 | D | B | 0.0000 | |
| 84 | T | B | -0.0792 | |
| 85 | G | B | -0.2286 | |
| 86 | T | B | -0.2147 | |
| 87 | Y | B | 0.0000 | |
| 88 | T | B | 0.0000 | |
| 89 | C | B | 0.0000 | |
| 90 | Q | B | 0.0000 | |
| 91 | A | B | 0.0000 | |
| 92 | I | B | -0.5490 | |
| 93 | T | B | -1.0334 | |
| 94 | E | B | -1.3721 | |
| 95 | V | B | 0.5471 | |
| 96 | N | B | -0.1827 | |
| 97 | V | B | -0.2183 | |
| 98 | Y | B | -0.3339 | |
| 99 | G | B | 0.0000 | |
| 100 | S | B | -0.9622 | |
| 101 | G | B | 0.0000 | |
| 102 | T | B | 0.0000 | |
| 103 | L | B | 0.0000 | |
| 104 | V | B | 0.0000 | |
| 105 | L | B | 0.0000 | |
| 106 | V | B | 0.0000 | |
| 107 | T | B | 0.0000 | |
| 108 | E | B | -2.9262 | |
| 109 | E | B | -3.4277 | |
| 110 | Q | B | -2.4637 | |
| 111 | S | B | -1.8382 | |
| 112 | Q | B | -2.6674 | |
| 113 | G | B | -1.7973 | |
| 114 | W | B | 0.0000 | |
| 115 | H | B | 0.0000 | |
| 116 | R | B | 0.0000 | |
| 117 | C | B | 0.0000 | |
| 118 | S | B | 0.0000 | |
| 119 | D | B | -0.4589 | |
| 120 | A | B | -0.5583 | |
| 121 | P | B | -0.7034 | |
| 122 | P | B | -1.1537 | |
| 123 | R | B | -1.9160 | |
| 124 | A | B | -0.8532 | |
| 125 | S | B | -0.5558 | |
| 126 | A | B | -0.0450 | |
| 127 | L | B | 0.2829 | |
| 128 | P | B | 0.0311 | |
| 129 | A | B | -0.1786 | |
| 130 | P | B | -0.4241 | |
| 131 | P | B | -0.6225 | |
| 132 | T | B | -0.5355 | |
| 133 | G | B | -0.4436 | |
| 134 | S | B | -0.0836 | |
| 135 | A | B | 0.1716 | |
| 136 | L | B | 0.7855 | |
| 137 | P | B | -0.6778 | |
| 138 | D | B | -1.9663 | |
| 139 | P | B | -1.5243 | |
| 140 | Q | B | -1.9359 | |
| 141 | T | B | -1.0430 | |
| 142 | A | B | -0.2126 | |
| 143 | S | B | 0.0109 | |
| 144 | A | B | 0.3543 | |
| 145 | L | B | 0.8997 | |
| 146 | P | B | -0.5008 | |
| 147 | D | B | -1.6841 | |
| 148 | P | B | -1.0519 | |
| 149 | P | B | -0.8773 | |
| 150 | A | B | -0.4393 | |
| 151 | A | B | 0.1197 | |
| 152 | S | B | 0.2178 | |
| 153 | A | B | 0.6666 | |
| 154 | L | B | 1.4035 | |
| 155 | P | B | 0.4725 |
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 | -0.3871 | 3.8219 | View | CSV | PDB |
| 4.5 | -0.4253 | 3.8219 | View | CSV | PDB |
| 5.0 | -0.4718 | 3.8219 | View | CSV | PDB |
| 5.5 | -0.5193 | 3.8219 | View | CSV | PDB |
| 6.0 | -0.5603 | 3.8219 | View | CSV | PDB |
| 6.5 | -0.5893 | 3.8219 | View | CSV | PDB |
| 7.0 | -0.6045 | 3.8219 | View | CSV | PDB |
| 7.5 | -0.6092 | 3.8219 | View | CSV | PDB |
| 8.0 | -0.6074 | 3.8219 | View | CSV | PDB |
| 8.5 | -0.5999 | 3.8219 | View | CSV | PDB |
| 9.0 | -0.5863 | 3.8219 | View | CSV | PDB |
ALA alanine
ARG arginine
ASN asparagine
ASP aspartic acid
CYS cysteine
GLN glutamine
GLU glutamic acid
GLY glycine
HIS histidine
ILE isoleucine
LEU leucine
LYS lysine
MET methionine
PHE phenylalanine
PRO proline
SER serine
THR threonine
TRP tryptophan
TYR tyrosine
VAL valine