Simulation report
Technical information
General information
Name: 5-ht2b receptor (apoform)
PDB id: 5TVN
Activation state: Intermediate
Submitted by: GPCRmd community
System setup
Solvent type: SPC
Membrane type: Homogeneous
Membrane composition: POP
Ionic composition: Sodium ion (6 mM)
Number of molecules:
Water: 10000
POPC: 283
Sodium ion: 1
5-hydroxytryptamine receptor 2B: 1
Total number of atoms: 124986
Simulation details
Software and version: GROMACS, v2018.3
Forcefield and version: Gromos, 54a7
Time step : 2.0 fs
Delta : 0.2 ns
Replicates: 1
Accumulated simulation time: 0.1002 µs
Additonal parameters: Available at "Simulation protocol & starting files"
References
Peters, Brandon L. and Deng, Jinxia and Ferguson, Andrew L., Garriga, Pere. 2020. Free energy calculations of the functional selectivity of 5-HT2B G protein-coupled receptor. PLOS ONE 15 (12). doi: 10.1371/journal.pone.0243313. (https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0243313)
GPCRmd publication page: 1518
Simulation components
Receptor
Mutations
Table of simulated mutations
(Mutations shown in blue at the viewer)
| Residue ID | Residue seq. position | Generic num. | From | To |
|---|---|---|---|---|
| 144 | 104 | 3x41 | M | W |
| 248 | 208 | 5x69 | Y | - |
| 248 | 208 | 5x69 | L | - |
| 248 | 208 | 5x69 | V | - |
| 248 | 208 | 5x69 | K | - |
| 248 | 208 | 5x69 | N | - |
| 248 | 208 | 5x69 | K | - |
| 248 | 208 | 5x69 | P | - |
| 248 | 208 | 5x69 | P | - |
| 248 | 208 | 5x69 | Q | - |
| 248 | 208 | 5x69 | R | - |
| 248 | 208 | 5x69 | L | - |
| 248 | 208 | 5x69 | T | - |
| 248 | 208 | 5x69 | W | - |
| 248 | 208 | 5x69 | L | - |
| 248 | 208 | 5x69 | T | - |
| 248 | 208 | 5x69 | V | - |
| 248 | 208 | 5x69 | S | - |
| 248 | 208 | 5x69 | T | - |
| 248 | 208 | 5x69 | V | - |
| 248 | 208 | 5x69 | F | - |
| 248 | 208 | 5x69 | Q | - |
| 248 | 208 | 5x69 | R | - |
| 248 | 208 | 5x69 | D | - |
| 248 | 208 | 5x69 | E | - |
| 248 | 208 | 5x69 | T | - |
| 248 | 208 | 5x69 | P | - |
| 248 | 208 | 5x69 | C | - |
| 248 | 208 | 5x69 | S | - |
| 248 | 208 | 5x69 | S | - |
| 248 | 208 | 5x69 | P | - |
| 248 | 208 | 5x69 | E | - |
| 248 | 208 | 5x69 | K | - |
| 248 | 208 | 5x69 | V | - |
| 248 | 208 | 5x69 | A | - |
| 248 | 208 | 5x69 | M | - |
| 248 | 208 | 5x69 | L | - |
| 248 | 208 | 5x69 | D | - |
| 248 | 208 | 5x69 | G | - |
| 248 | 208 | 5x69 | S | - |
| 248 | 208 | 5x69 | R | - |
| 248 | 208 | 5x69 | K | - |
| 248 | 208 | 5x69 | D | - |
| 248 | 208 | 5x69 | K | - |
| 248 | 208 | 5x69 | A | - |
| 248 | 208 | 5x69 | L | - |
| 248 | 208 | 5x69 | P | - |
| 248 | 208 | 5x69 | N | - |
| 248 | 208 | 5x69 | S | - |
| 248 | 208 | 5x69 | G | - |
| 248 | 208 | 5x69 | D | - |
| 248 | 208 | 5x69 | E | - |
| 248 | 208 | 5x69 | T | - |
| 248 | 208 | 5x69 | L | - |
| 248 | 208 | 5x69 | M | - |
| 248 | 208 | 5x69 | R | - |
| 248 | 208 | 5x69 | R | - |
| 248 | 208 | 5x69 | T | - |
| 248 | 208 | 5x69 | S | - |
| 248 | 208 | 5x69 | T | - |
| 248 | 208 | 5x69 | I | - |
| 248 | 208 | 5x69 | G | - |
| 248 | 208 | 5x69 | K | - |
| 248 | 208 | 5x69 | K | - |
| 248 | 208 | 5x69 | S | - |
| 1001 | 209 | - | - | A |
| 1002 | 210 | - | - | D |
| 1003 | 211 | - | - | L |
| 1004 | 212 | - | - | E |
| 1005 | 213 | - | - | D |
| 1006 | 214 | - | - | N |
| 1007 | 215 | - | - | W |
| 1008 | 216 | - | - | E |
| 1009 | 217 | - | - | T |
| 1010 | 218 | - | - | L |
| 1011 | 219 | - | - | N |
| 1012 | 220 | - | - | D |
| 1013 | 221 | - | - | N |
| 1014 | 222 | - | - | L |
| 1015 | 223 | - | - | K |
| 1016 | 224 | - | - | V |
| 1017 | 225 | - | - | I |
| 1018 | 226 | - | - | E |
| 1019 | 227 | - | - | K |
| 1020 | 228 | - | - | A |
| 1021 | 229 | - | - | D |
| 1022 | 230 | - | - | N |
| 1023 | 231 | - | - | A |
| 1024 | 232 | - | - | A |
| 1025 | 233 | - | - | Q |
| 1026 | 234 | - | - | V |
| 1027 | 235 | - | - | K |
| 1028 | 236 | - | - | D |
| 1029 | 237 | - | - | A |
| 1030 | 238 | - | - | L |
| 1031 | 239 | - | - | T |
| 1032 | 240 | - | - | K |
| 1033 | 241 | - | - | M |
| 1034 | 242 | - | - | R |
| 1035 | 243 | - | - | A |
| 1036 | 244 | - | - | A |
| 1037 | 245 | - | - | A |
| 1038 | 246 | - | - | L |
| 1039 | 247 | - | - | D |
| 1040 | 248 | - | - | A |
| 1041 | 249 | - | - | Q |
| 1042 | 250 | - | - | K |
| 1043 | 251 | - | - | A |
| 1044 | 252 | - | - | T |
| 1045 | 253 | - | - | P |
| 1046 | 254 | - | - | P |
| 1047 | 255 | - | - | K |
| 1048 | 256 | - | - | L |
| 1049 | 257 | - | - | E |
| 1050 | 258 | - | - | D |
| 1051 | 259 | - | - | K |
| 1052 | 260 | - | - | S |
| 1053 | 261 | - | - | P |
| 1054 | 262 | - | - | D |
| 1055 | 263 | - | - | S |
| 1056 | 264 | - | - | P |
| 1057 | 265 | - | - | E |
| 1058 | 266 | - | - | M |
| 1059 | 267 | - | - | K |
| 1060 | 268 | - | - | D |
| 1061 | 269 | - | - | F |
| 1062 | 270 | - | - | R |
| 1063 | 271 | - | - | H |
| 1064 | 272 | - | - | G |
| 1065 | 273 | - | - | F |
| 1066 | 274 | - | - | D |
| 1067 | 275 | - | - | I |
| 1068 | 276 | - | - | L |
| 1069 | 277 | - | - | V |
| 1070 | 278 | - | - | G |
| 1071 | 279 | - | - | Q |
| 1072 | 280 | - | - | I |
| 1073 | 281 | - | - | D |
| 1074 | 282 | - | - | D |
| 1075 | 283 | - | - | A |
| 1076 | 284 | - | - | L |
| 1077 | 285 | - | - | K |
| 1078 | 286 | - | - | L |
| 1079 | 287 | - | - | A |
| 1080 | 288 | - | - | N |
| 1081 | 289 | - | - | E |
| 1082 | 290 | - | - | G |
| 1083 | 291 | - | - | K |
| 1084 | 292 | - | - | V |
| 1085 | 293 | - | - | K |
| 1086 | 294 | - | - | E |
| 1087 | 295 | - | - | A |
| 1088 | 296 | - | - | Q |
| 1089 | 297 | - | - | A |
| 1090 | 298 | - | - | A |
| 1091 | 299 | - | - | A |
| 1092 | 300 | - | - | E |
| 1093 | 301 | - | - | Q |
| 1094 | 302 | - | - | L |
| 1095 | 303 | - | - | K |
| 1096 | 304 | - | - | T |
| 1097 | 305 | - | - | T |
| 1098 | 306 | - | - | R |
| 1099 | 307 | - | - | N |
| 1100 | 308 | - | - | A |
| 1101 | 309 | - | - | Y |
| 1102 | 310 | - | - | I |
| 1103 | 311 | - | - | Q |
| 1104 | 312 | - | - | K |
| 1105 | 313 | - | - | Y |
| 1106 | 314 | - | - | L |
