8AW2

Mouse serotonin 5-HT3A receptor in complex with vortioxetine

PDB DOI: https://doi.org/10.2210/pdb8AW2/pdb
EM Map EMD-15689: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Mus musculus
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes PDBTM

Deposited: 2022-08-29 Released: 2024-03-06
Deposition Author(s): Lopez-Sanchez, U., Nury, H.
Funding Organization(s): European Research Council (ERC)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.01 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Mouse serotonin 5-HT3A receptor in complex with vortioxetine

Lopez-Sanchez, U., Nury, H.

To be published.

Macromolecule Content

Total Structure Weight: 326.66 kDa
Atom Count: 16,375
Modelled Residue Count: 1,920
Deposited Residue Count: 2,830
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 3A	A, B, C, D, E	566	Mus musculus	Mutation(s): 0 Gene Names: Htr3a, 5ht3, Htr3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23979 (Mus musculus) Explore P23979 Go to UniProtKB: P23979
IMPC: MGI:96282
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23979
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, H, J, L, N	3		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain J Focus chain L Focus chain N Interactions & Density Focus chain F Focus chain H Focus chain J Focus chain L Focus chain N
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, I, K, M, O	2		N-Glycosylation	Interactions Focus chain G Focus chain I Focus chain K Focus chain M Focus chain O Interactions & Density Focus chain G Focus chain I Focus chain K Focus chain M Focus chain O
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VTX (Subject of Investigation/LOI) Query on VTX Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain DA [auth E] SDF format, chain R [auth A] SDF format, chain U [auth B] SDF format, chain X [auth C] MOL2 format, chain AA [auth D] MOL2 format, chain DA [auth E] MOL2 format, chain R [auth A] MOL2 format, chain U [auth B] MOL2 format, chain X [auth C]	AA [auth D], DA [auth E], R [auth A], U [auth B], X [auth C]	Vortioxetine C₁₈ H₂₂ N₂ S YQNWZWMKLDQSAC-UHFFFAOYSA-N		Interactions Focus chain AA [auth D] Focus chain DA [auth E] Focus chain R [auth A] Focus chain U [auth B] Focus chain X [auth C] Interactions & Density Focus chain AA [auth D] Focus chain DA [auth E] Focus chain R [auth A] Focus chain U [auth B] Focus chain X [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain BA [auth E] SDF format, chain P [auth A] SDF format, chain S [auth B] SDF format, chain V [auth C] SDF format, chain Y [auth D] MOL2 format, chain BA [auth E] MOL2 format, chain P [auth A] MOL2 format, chain S [auth B] MOL2 format, chain V [auth C] MOL2 format, chain Y [auth D]	BA [auth E], P [auth A], S [auth B], V [auth C], Y [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth E] Focus chain P [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain Y [auth D] Interactions & Density Focus chain BA [auth E] Focus chain P [auth A] Focus chain S [auth B] Focus chain V [auth C] Focus chain Y [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain CA [auth E] SDF format, chain Q [auth A] SDF format, chain T [auth B] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain CA [auth E] MOL2 format, chain Q [auth A] MOL2 format, chain T [auth B] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D]	CA [auth E], Q [auth A], T [auth B], W [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain CA [auth E] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain CA [auth E] Focus chain Q [auth A] Focus chain T [auth B] Focus chain W [auth C] Focus chain Z [auth D]