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Simulation report

Technical information

General information

Name: 5-ht2b receptor (apoform)

PDB id: 5TVN

Activation state: Intermediate

Description: -

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"



Simulation components

Receptor

Visualization and trajectory sharing powered by NGL viewer and MDSrv

Open with GPCRmd Workbench

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


Other molecules



Sodium ion

Specific State ID: 5016

(1 molecule)

Na+


POPC

Specific State ID: 5018

(283 molecules)


Water

Specific State ID: 5019

(10000 molecules)

H2O