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"



Simulation components

Receptor

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Open with GPCRmd Workbench

Mutations

Table of simulated mutations

(Mutations shown in blue at the viewer)

Residue Generic num. From To
104 3x41 M W
208 5x69 Y -
208 5x69 L -
208 5x69 V -
208 5x69 K -
208 5x69 N -
208 5x69 K -
208 5x69 P -
208 5x69 P -
208 5x69 Q -
208 5x69 R -
208 5x69 L -
208 5x69 T -
208 5x69 W -
208 5x69 L -
208 5x69 T -
208 5x69 V -
208 5x69 S -
208 5x69 T -
208 5x69 V -
208 5x69 F -
208 5x69 Q -
208 5x69 R -
208 5x69 D -
208 5x69 E -
208 5x69 T -
208 5x69 P -
208 5x69 C -
208 5x69 S -
208 5x69 S -
208 5x69 P -
208 5x69 E -
208 5x69 K -
208 5x69 V -
208 5x69 A -
208 5x69 M -
208 5x69 L -
208 5x69 D -
208 5x69 G -
208 5x69 S -
208 5x69 R -
208 5x69 K -
208 5x69 D -
208 5x69 K -
208 5x69 A -
208 5x69 L -
208 5x69 P -
208 5x69 N -
208 5x69 S -
208 5x69 G -
208 5x69 D -
208 5x69 E -
208 5x69 T -
208 5x69 L -
208 5x69 M -
208 5x69 R -
208 5x69 R -
208 5x69 T -
208 5x69 S -
208 5x69 T -
208 5x69 I -
208 5x69 G -
208 5x69 K -
208 5x69 K -
208 5x69 S -
209 - - A
210 - - D
211 - - L
212 - - E
213 - - D
214 - - N
215 - - W
216 - - E
217 - - T
218 - - L
219 - - N
220 - - D
221 - - N
222 - - L
223 - - K
224 - - V
225 - - I
226 - - E
227 - - K
228 - - A
229 - - D
230 - - N
231 - - A
232 - - A
233 - - Q
234 - - V
235 - - K
236 - - D
237 - - A
238 - - L
239 - - T
240 - - K
241 - - M
242 - - R
243 - - A
244 - - A
245 - - A
246 - - L
247 - - D
248 - - A
249 - - Q
250 - - K
251 - - A
252 - - T
253 - - P
254 - - P
255 - - K
256 - - L
257 - - E
258 - - D
259 - - K
260 - - S
261 - - P
262 - - D
263 - - S
264 - - P
265 - - E
266 - - M
267 - - K
268 - - D
269 - - F
270 - - R
271 - - H
272 - - G
273 - - F
274 - - D
275 - - I
276 - - L
277 - - V
278 - - G
279 - - Q
280 - - I
281 - - D
282 - - D
283 - - A
284 - - L
285 - - K
286 - - L
287 - - A
288 - - N
289 - - E
290 - - G
291 - - K
292 - - V
293 - - K
294 - - E
295 - - A
296 - - Q
297 - - A
298 - - A
299 - - A
300 - - E
301 - - Q
302 - - L
303 - - K
304 - - T
305 - - T
306 - - R
307 - - N
308 - - A
309 - - Y
310 - - I
311 - - Q
312 - - K
313 - - Y
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