9WNG: 5HT2BR-fab heterotrimer

5HT2BR-fab heterotrimer in complex with a novel antagonist IHCH-2330. Determined by electron microscopy at 2.98 Å resolution. Released 9 Sept 2026.

Method: Electron microscopy
Resolution: 2.98 Å
Organism: Homo sapiens
Chains: 3
Atoms: 5,054
Mol. weight: 90.02 kDa
Ligands: NAG, A1EXY
Released: 9 Sept 2026

Explore 9WNG in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

9WNG contains 28 α-helices and 44 β-strands across 3 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain B: 6 helices, 21 β-strands

Element	Residues	Length	Sheet
β-strand	4-7	4	1
β-strand	10-12	3	2
β-strand	19-25	7	1
β-strand	32-37	6	2
β-strand	44-48	5	2
β-strand	52-53	2	2
β-strand	61-65	5	1
β-strand	69-74	6	1
α-helix	79-81	3
β-strand	84-89	6	2
α-helix	95	1
β-strand	96	1	2
β-strand	101-104	4	2
β-strand	110	1	3
β-strand	113-117	5	4
α-helix	118-120	3
α-helix	121-124	4
β-strand	128-138	11	4
β-strand	139	1	3
β-strand	143-149	7	5
β-strand	153	1	5
β-strand	162	1	4
α-helix	163-166	4
β-strand	172-181	10	4
α-helix	182-186	5
β-strand	190-197	8	5
β-strand	205-209	5	5

Chain C: 7 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	6
α-helix	7-9	3
β-strand	10-12	3	7
β-strand	18	1	6
β-strand	21-25	5	6
α-helix	29-31	3
β-strand	34-40	7	7
β-strand	44-51	8	7
β-strand	58-60	3	7
α-helix	62-64	3
β-strand	68-73	6	6
β-strand	78-83	6	6
α-helix	88-90	3
β-strand	92-98	7	7
β-strand	101-104	4	8
β-strand	109-112	4	8
β-strand	116-117	2	7
β-strand	121-125	5	7
β-strand	134-137	4	9
β-strand	150-157	8	9
β-strand	164-168	5	10
β-strand	173	1	10
β-strand	177-179	3	9
α-helix	180-182	3
β-strand	193-198	6	9
α-helix	200-202	3
β-strand	209-214	6	10
α-helix	215-217	3
β-strand	219-224	6	10

Chain R: 15 helices, 1 β-strand

Element	Residues	Length	Sheet
α-helix	57-81	25
α-helix	88-102	15
α-helix	103-107	5
α-helix	108-116	9
α-helix	127-156	30
α-helix	169-187	19
α-helix	189-192	4
β-strand	195-197	3	8
α-helix	202-204	3
α-helix	216-222	7
α-helix	223-227	5
α-helix	228-243	16
α-helix	323-349	27
α-helix	355-377	23
α-helix	378-382	5
α-helix	385-393	9

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
P2C2 Fab light chain	B	protein	236	Homo sapiens
P2C2 Fab heavy chain	C	protein	270	Homo sapiens
5-hydroxytryptamine receptor 2B	R	protein	307	Homo sapiens	P41595 (AlphaFold model)

Sequence of entity 1 (B), FASTA

>9WNG_1 P2C2 Fab light chain (chains B)
MKKNIAFLLASMFVFSIATNAYADIVLIQSPAIMSASPGEKVTITCSASSSVSYMHWFQQ
KPGTSPKLWIYSTSNLASGVPARFSGSGSGTSYSLTISRMEAEDAATYYCQQRSSYPLTF
GAGTKLEIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGN
SQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSLPVTKSFNRGEC

Sequence of entity 2 (C), FASTA

>9WNG_2 P2C2 Fab heavy chain (chains C)
MKKNIAFLLASMFVFSIATNAYAEVQLQQSGPELVKPGASVKLSCKASGYTFTSSWMHWV
KQRPGQGLEWIGNIYPSNGGTNYNERFKSKATLTVDRSSNTAYMQLSSLTSEDSAVYFCA
RFGSFITTILTTYYNPVDYWGQGTTLTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVK
DYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPS
NTKVDKKVEPKSCENLYFQSGSHHHHHHHH

Sequence of entity 3 (R), FASTA

>9WNG_3 5-hydroxytryptamine receptor 2B (chains R)
GPGSGSGTESIPEEMKQIVEEQGNKLHWAALLILMVIIPTIGGNTLVILAVSLEKKLQYA
TNYFLMSLAVADLLVGLFVMPIALLTIMFEAMWPLPLVLCPAWLFLDVLFSTASIWHLCA
ISVDRYIAIKKPIQANQYNSRATAFIKITVVWLISIGIAIPVPIKGIETDVDNPNNITCV
LTKERFGDFMLFGSLAAFFTPLAIMIVTYFLTIHALQKKRLLSGSRQTISNEQRASKVLG
IVFFLFLLMWCPFFITNITLVLCDSCNQTTLQMLLEIFVWIGYVSSGVNPLVYTLFNKTF
RDAFGRY

Ligands and cofactors

ID	Name	Formula	Copies
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1
A1EXY	3-[2-[2-[2,5-dimethoxy-4-(trifluoromethyl)phenyl]ethyl-methyl-amino]ethyl]-2-me…	C23 H26 F3 N3 O3	1

Primary citation

Mechanistic Basis for 5-HT 2A R Over 5-HT 2B R Activation. Tang, L., Ji, X., Wang, Y. et al. Nat Commun (2026) 17. DOI 10.1038/s41467-026-77659-x · PubMed

Other PDB entries of the same protein (UniProt P41595 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4IB4 2.7 Å, Crystal structure of the chimeric protein of 5-HT2B-BRIL in complex with ergotamine
7SRQ 2.7 Å, 5-HT2B receptor bound to LSD obtained by cryo-electron microscopy (cryoEM)
4NC3 2.8 Å, Crystal structure of the 5-HT2B receptor solved using serial femtosecond crystallography…
5TVN 2.9 Å, Crystal structure of the LSD-bound 5-HT2B receptor
7SRR 2.9 Å, 5-HT2B receptor bound to LSD in complex with heterotrimeric mini-Gq protein obtained by…
6DRY 2.92 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
5TUD 3.0 Å, Structural Insights into the Extracellular Recognition of the Human Serotonin 2B…
6DRX 3.1 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
6DRZ 3.1 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
9WQB 3.18 Å, 5-HT2B receptor bound to IHCH-6122 in complex with an antibody obtained by cryo-electron…
6DS0 3.19 Å, Structural Determinants of Activation and Biased Agonism at the 5-HT2B Receptor
9WQA 3.28 Å, 5-HT2B receptor bound to IHCH-1906 in complex with an antibody obtained by cryo-electron…

Browse structure collections

About this viewer

MolViewer shows 9WNG directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.