| Chain sequence(s) | QIVLTQSPAIMSASLGERVTMTCTASSSVYSSYLHWYQQKPGSSPKLWIYSTSNLASGVPGRFSGSGSGTSYSLTISSMEAEDAATYYCHQYHRSPTFGGGTKLEIKGGGGSGGGGSGGGGSQVQLQQSGAELVRPGTSVKISCKASGYDFTNYWLGWVKQRPGHGLEWIGDIYPGGGNTYYNEKLKGKATLTADKSSSTAYIHLISLTSEDSSVYFCARWGDKKGNYFAYWGQGTLTVSS input PDB |
| Selected Chain(s) | A |
| Distance of aggregation | 10 Å |
| FoldX usage | Yes |
| pH calculations | Yes |
| 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 (00:02:17)
[INFO] agg3D: Running pKa-ANI on
/STORAGE/DATA/lcbio/aggreskan/135a64462711ca/tmp/folded.pdb (00:02:17)
[INFO] Main: Simulation completed successfully. (00:03:30)
|
The table below lists A3D score for protein residues. Residues with A3D score > 0.0000 are marked by yellow rows.
| residue index | residue name | chain | Aggrescan3D score | mutation |
|---|---|---|---|---|
| residue index | residue name | chain | Aggrescan3D score | |
| 1 | Q | A | -1.2846 | |
| 2 | I | A | 0.0752 | |
| 3 | V | A | 1.4317 | |
| 4 | L | A | 0.0000 | |
| 5 | T | A | 0.1705 | |
| 6 | Q | A | 0.0000 | |
| 7 | S | A | -0.0358 | |
| 8 | P | A | 0.2726 | |
| 9 | A | A | 0.5711 | |
| 10 | I | A | 1.3331 | |
| 11 | M | A | 0.2016 | |
| 12 | S | A | -1.0336 | |
| 13 | A | A | 0.0000 | |
| 14 | S | A | -1.2006 | |
| 15 | L | A | -0.0057 | |
| 16 | G | A | -1.1759 | |
| 17 | E | A | -2.2201 | |
| 18 | R | A | -2.5399 | |
| 19 | V | A | 0.0000 | |
| 20 | T | A | -0.6498 | |
| 21 | M | A | 0.0000 | |
| 22 | T | A | -0.2212 | |
| 23 | C | A | 0.0000 | |
| 24 | T | A | -0.0752 | |
| 25 | A | A | 0.0000 | |
| 26 | S | A | 0.0922 | |
| 27 | S | A | -0.2091 | |
| 28 | S | A | -0.1935 | |
| 29 | V | A | 0.0000 | |
| 30 | Y | A | 1.1706 | |
| 31 | S | A | 0.4119 | |
| 32 | S | A | 0.3727 | |
| 33 | Y | A | 0.7996 | |
| 34 | L | A | 0.0000 | |
| 35 | H | A | 0.0000 | |
| 36 | W | A | 0.0000 | |
| 37 | Y | A | 0.0000 | |
| 38 | Q | A | 0.0000 | |
| 39 | Q | A | -0.9903 | |
| 40 | K | A | -1.4829 | |
| 41 | P | A | -0.8981 | |
| 42 | G | A | -0.9927 | |
| 43 | S | A | -1.0942 | |
| 44 | S | A | -0.9624 | |
| 45 | P | A | 0.0000 | |
| 46 | K | A | -1.6325 | |
| 47 | L | A | 0.0000 | |
| 48 | W | A | -0.3620 | |
| 49 | I | A | 0.0000 | |
| 50 | Y | A | 0.1969 | |
| 51 | S | A | 0.1276 | |
| 52 | T | A | 0.0000 | |
| 53 | S | A | -0.5472 | |
| 54 | N | A | -0.6070 | |
| 55 | L | A | -0.0452 | |
| 56 | A | A | -0.2486 | |
| 57 | S | A | -0.3490 | |
| 58 | G | A | -0.5713 | |
| 59 | V | A | -0.2340 | |
| 60 | P | A | -0.3634 | |
| 61 | G | A | -0.6305 | |
| 62 | R | A | -1.0067 | |
| 63 | F | A | 0.0000 | |
| 64 | S | A | -0.5002 | |
| 65 | G | A | 0.0000 | |
| 66 | S | A | -0.6121 | |
| 67 | G | A | -0.4788 | |
| 68 | S | A | -0.3229 | |
| 69 | G | A | -0.2259 | |
| 70 | T | A | -0.3132 | |
| 71 | S | A | -0.5439 | |
| 72 | Y | A | 0.0000 | |
| 73 | S | A | -0.3231 | |
| 74 | L | A | 0.0000 | |
| 75 | T | A | -0.6063 | |
| 76 | I | A | 0.0000 | |
| 77 | S | A | -1.6585 | |
| 78 | S | A | -1.5878 | |
| 79 | M | A | 0.0000 | |
| 80 | E | A | -1.6560 | |
| 81 | A | A | -1.4909 | |
| 82 | E | A | -2.4739 | |
| 83 | D | A | 0.0000 | |
| 84 | A | A | -1.6160 | |
| 85 | A | A | 0.0000 | |
| 86 | T | A | -0.5504 | |
| 87 | Y | A | 0.0000 | |
| 88 | Y | A | 0.0000 | |
| 89 | C | A | 0.0000 | |
| 90 | H | A | 0.0000 | |
| 91 | Q | A | 0.0000 | |
| 92 | Y | A | -0.0865 | |
| 93 | H | A | -1.0348 | |
| 94 | R | A | -2.0213 | |
| 95 | S | A | -1.3079 | |
| 96 | P | A | 0.0000 | |
| 97 | T | A | -0.1468 | |
| 98 | F | A | 0.1824 | |
| 99 | G | A | 0.0000 | |
| 100 | G | A | -0.7217 | |
| 101 | G | A | 0.0000 | |
| 102 | T | A | 0.0000 | |
| 103 | K | A | -0.6191 | |
| 104 | L | A | 0.0000 | |
| 105 | E | A | -1.7906 | |
| 106 | I | A | -1.6170 | |
| 107 | K | A | -2.0982 | |
| 108 | G | A | -1.7809 | |
| 109 | G | A | -1.6912 | |
| 110 | G | A | -1.4366 | |
| 111 | G | A | -1.3105 | |
| 112 | S | A | -0.9970 | |
| 113 | G | A | -1.5862 | |
| 114 | G | A | -1.5860 | |
| 115 | G | A | -1.5349 | |
| 116 | G | A | -1.4130 | |
| 117 | S | A | -0.9838 | |
| 118 | G | A | -1.2935 | |
| 119 | G | A | -1.3190 | |
| 120 | G | A | -1.3595 | |
| 121 | G | A | -1.3863 | |
| 122 | S | A | -1.3219 | |
| 123 | Q | A | -1.9254 | |
| 124 | V | A | 0.0000 | |
| 125 | Q | A | -1.5743 | |
| 126 | L | A | 0.0000 | |
| 127 | Q | A | -1.8000 | |
| 128 | Q | A | 0.0000 | |
| 129 | S | A | -0.9634 | |
| 130 | G | A | -0.7495 | |
| 131 | A | A | 0.2675 | |
| 132 | E | A | -0.0977 | |
| 133 | L | A | 1.1413 | |
| 134 | V | A | -0.2344 | |
| 135 | R | A | -1.7573 | |
| 136 | P | A | -1.4042 | |
| 137 | G | A | -0.9767 | |
| 138 | T | A | -0.7575 | |
| 139 | S | A | -0.6858 | |
| 140 | V | A | 0.0000 | |
| 141 | K | A | -1.5853 | |
| 142 | I | A | 0.0000 | |
| 143 | S | A | -0.8406 | |
| 144 | C | A | 0.0000 | |
| 145 | K | A | -1.6153 | |
| 146 | A | A | 0.0000 | |
| 147 | S | A | -1.4631 | |
| 148 | G | A | -1.4529 | |
| 149 | Y | A | -1.2871 | |
| 150 | D | A | -2.1023 | |
| 151 | F | A | 0.0000 | |
| 152 | T | A | -1.2840 | |
| 153 | N | A | -1.5507 | |
| 154 | Y | A | -1.2314 | |
| 155 | W | A | -0.7439 | |
| 156 | L | A | 0.0000 | |
| 157 | G | A | 0.0000 | |
| 158 | W | A | 0.0000 | |
| 159 | V | A | 0.0000 | |
| 160 | K | A | 0.0000 | |
| 161 | Q | A | -0.8615 | |
| 162 | R | A | -1.6034 | |
| 163 | P | A | -1.2834 | |
| 164 | G | A | -1.2822 | |
| 165 | H | A | -1.8203 | |
| 166 | G | A | -1.2450 | |
| 167 | L | A | 0.0000 | |
| 168 | E | A | -1.2047 | |
| 169 | W | A | 0.0000 | |
| 170 | I | A | 0.0000 | |
| 171 | G | A | 0.0000 | |
| 172 | D | A | 0.0000 | |
| 173 | I | A | 0.0000 | |
| 174 | Y | A | -0.4916 | |
| 175 | P | A | 0.0000 | |
| 176 | G | A | -1.3041 | |
| 177 | G | A | -1.1668 | |
| 178 | G | A | -1.5137 | |
| 179 | N | A | -1.3072 | |
| 180 | T | A | -0.0440 | |
| 181 | Y | A | 0.5007 | |
| 182 | Y | A | -0.5208 | |
| 183 | N | A | -1.9334 | |
| 184 | E | A | -3.2675 | |
| 185 | K | A | -3.1246 | |
| 186 | L | A | -2.2922 | |
| 187 | K | A | -2.9109 | |
| 188 | G | A | -1.7847 | |
| 189 | K | A | -1.3117 | |
| 190 | A | A | 0.0000 | |
| 191 | T | A | -0.6349 | |
| 192 | L | A | 0.0000 | |
| 193 | T | A | -0.5801 | |
| 194 | A | A | -1.0240 | |
| 195 | D | A | -1.7908 | |
| 196 | K | A | -2.4682 | |
| 197 | S | A | -1.3316 | |
| 198 | S | A | -1.2237 | |
| 199 | S | A | -1.5848 | |
| 200 | T | A | 0.0000 | |
| 201 | A | A | 0.0000 | |
| 202 | Y | A | -0.5162 | |
| 203 | I | A | 0.0000 | |
| 204 | H | A | -0.8764 | |
| 205 | L | A | 0.0000 | |
| 206 | I | A | 0.0401 | |
| 207 | S | A | -0.4437 | |
| 208 | L | A | 0.0000 | |
| 209 | T | A | -1.1268 | |
| 210 | S | A | -1.3640 | |
| 211 | E | A | -2.0468 | |
| 212 | D | A | 0.0000 | |
| 213 | S | A | -0.3684 | |
| 214 | S | A | 0.0000 | |
| 215 | V | A | 0.4921 | |
| 216 | Y | A | 0.0000 | |
| 217 | F | A | 0.0000 | |
| 218 | C | A | 0.0000 | |
| 219 | A | A | 0.0000 | |
| 220 | R | A | 0.0000 | |
| 221 | W | A | 0.0000 | |
| 222 | G | A | -0.7695 | |
| 223 | D | A | -1.9662 | |
| 224 | K | A | -2.8242 | |
| 225 | K | A | -2.7422 | |
| 226 | G | A | -1.5306 | |
| 227 | N | A | -0.7249 | |
| 228 | Y | A | 0.0259 | |
| 229 | F | A | 0.0000 | |
| 230 | A | A | -0.0818 | |
| 231 | Y | A | -0.1355 | |
| 232 | W | A | -0.5209 | |
| 233 | G | A | 0.0000 | |
| 234 | Q | A | -1.4192 | |
| 235 | G | A | -0.5648 | |
| 236 | T | A | 0.0000 | |
| 237 | L | A | 0.8973 | |
| 238 | T | A | 0.0000 | |
| 239 | V | A | 0.5835 | |
| 240 | S | A | -0.5177 | |
| 241 | S | A | -0.3980 |
Calculations for various pH values
This page contains details and comparisons for all models calculated at different pH points.
pH |
Average A3D Score |
Max A3D Score |
|||
| 4.0 | -0.725 | 2.3632 | View | CSV | PDB |
| 4.5 | -0.7539 | 2.3247 | View | CSV | PDB |
| 5.0 | -0.7883 | 2.2725 | View | CSV | PDB |
| 5.5 | -0.8189 | 2.2195 | View | CSV | PDB |
| 6.0 | -0.8349 | 2.1841 | View | CSV | PDB |
| 6.5 | -0.8288 | 2.1877 | View | CSV | PDB |
| 7.0 | -0.8013 | 2.239 | View | CSV | PDB |
| 7.5 | -0.7601 | 2.3241 | View | CSV | PDB |
| 8.0 | -0.7117 | 2.4249 | View | CSV | PDB |
| 8.5 | -0.659 | 2.5312 | View | CSV | PDB |
| 9.0 | -0.6044 | 2.6389 | 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