9IY7 | pdb_00009iy7

Cryo-EM structure of the wild-type human serotonin transporter complexed with S-ketamine

PDB DOI: https://doi.org/10.2210/pdb9IY7/pdb
EM Map EMD-60987: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Homo sapiens
Mutation(s): No

Deposited: 2024-07-30 Released: 2025-11-12
Deposition Author(s): Ning, Y., Ge, J.
Funding Organization(s): Other government

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.27 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 of the entry. See complete history.

Literature

CryoEM structure of a transmembrane protein

Ning, Y., Ge, J.

To be published.

Macromolecule Content

Total Structure Weight: 76.13 kDa
Atom Count: 4,664
Modeled Residue Count: 540
Deposited Residue Count: 636
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sodium-dependent serotonin transporter	A	636	Homo sapiens	Mutation(s): 0 Gene Names: SLC6A4, HTT, SERT
UniProt & NIH Common Fund Data Resources
Find proteins for P31645 (Homo sapiens) Explore P31645 Go to UniProtKB: P31645
PHAROS: P31645 GTEx: ENSG00000108576
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P31645
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A	Go to GlyGen: P31645-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 10 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LMT Query on LMT Download Ideal Coordinates CCD File SDF format, chain G [auth A] MOL2 format, chain G [auth A] mmCIF format, chain G [auth A]	G [auth A]	DODECYL-BETA-D-MALTOSIDE C₂₄ H₄₆ O₁₁ NLEBIOOXCVAHBD-QKMCSOCLSA-N		Interactions Focus chain G [auth A] Interactions & Density Focus chain G [auth A]
Y01 Query on Y01 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain W [auth A] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain W [auth A] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain W [auth A]	E [auth A], F [auth A], W [auth A]	CHOLESTEROL HEMISUCCINATE C₃₁ H₅₀ O₄ WLNARFZDISHUGS-MIXBDBMTSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth A] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain W [auth A]
JC9 (Subject of Investigation/LOI) Query on JC9 Download Ideal Coordinates CCD File SDF format, chain I [auth A] MOL2 format, chain I [auth A] mmCIF format, chain I [auth A]	I [auth A]	(2~{S})-2-(2-chlorophenyl)-2-(methylamino)cyclohexan-1-one C₁₃ H₁₆ Cl N O YQEZLKZALYSWHR-ZDUSSCGKSA-N		Interactions Focus chain I [auth A] Interactions & Density Focus chain I [auth A]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain H [auth A] MOL2 format, chain H [auth A] mmCIF format, chain H [auth A]	H [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain H [auth A] Interactions & Density Focus chain H [auth A]
D12 Query on D12 Download Ideal Coordinates CCD File SDF format, chain AA [auth A] SDF format, chain L [auth A] SDF format, chain N [auth A] SDF format, chain T [auth A] SDF format, chain V [auth A] SDF format, chain Y [auth A] MOL2 format, chain AA [auth A] MOL2 format, chain L [auth A] MOL2 format, chain N [auth A] MOL2 format, chain T [auth A] MOL2 format, chain V [auth A] MOL2 format, chain Y [auth A] mmCIF format, chain AA [auth A] mmCIF format, chain L [auth A] mmCIF format, chain N [auth A] mmCIF format, chain T [auth A] mmCIF format, chain V [auth A] mmCIF format, chain Y [auth A]	AA [auth A] L [auth A] N [auth A] T [auth A] V [auth A] AA [auth A], L [auth A], N [auth A], T [auth A], V [auth A], Y [auth A]	DODECANE C₁₂ H₂₆ SNRUBQQJIBEYMU-UHFFFAOYSA-N		Interactions Focus chain AA [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain Y [auth A] Interactions & Density Focus chain AA [auth A] Focus chain L [auth A] Focus chain N [auth A] Focus chain T [auth A] Focus chain V [auth A] Focus chain Y [auth A]
D10 Query on D10 Download Ideal Coordinates CCD File SDF format, chain O [auth A] SDF format, chain U [auth A] MOL2 format, chain O [auth A] MOL2 format, chain U [auth A] mmCIF format, chain O [auth A] mmCIF format, chain U [auth A]	O [auth A], U [auth A]	DECANE C₁₀ H₂₂ DIOQZVSQGTUSAI-UHFFFAOYSA-N		Interactions Focus chain O [auth A] Focus chain U [auth A] Interactions & Density Focus chain O [auth A] Focus chain U [auth A]
DD9 Query on DD9 Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain M [auth A] SDF format, chain X [auth A] SDF format, chain Z [auth A] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain M [auth A] MOL2 format, chain X [auth A] MOL2 format, chain Z [auth A] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain M [auth A] mmCIF format, chain X [auth A] mmCIF format, chain Z [auth A]	J [auth A], K [auth A], M [auth A], X [auth A], Z [auth A]	nonane C₉ H₂₀ BKIMMITUMNQMOS-UHFFFAOYSA-N		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain X [auth A] Focus chain Z [auth A] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain M [auth A] Focus chain X [auth A] Focus chain Z [auth A]
OCT Query on OCT Download Ideal Coordinates CCD File SDF format, chain BA [auth A] SDF format, chain P [auth A] SDF format, chain Q [auth A] SDF format, chain R [auth A] SDF format, chain S [auth A] MOL2 format, chain BA [auth A] MOL2 format, chain P [auth A] MOL2 format, chain Q [auth A] MOL2 format, chain R [auth A] MOL2 format, chain S [auth A] mmCIF format, chain BA [auth A] mmCIF format, chain P [auth A] mmCIF format, chain Q [auth A] mmCIF format, chain R [auth A] mmCIF format, chain S [auth A]	BA [auth A], P [auth A], Q [auth A], R [auth A], S [auth A]	N-OCTANE C₈ H₁₈ TVMXDCGIABBOFY-UHFFFAOYSA-N		Interactions Focus chain BA [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A] Interactions & Density Focus chain BA [auth A] Focus chain P [auth A] Focus chain Q [auth A] Focus chain R [auth A] Focus chain S [auth A]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A]	C [auth A], D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain D [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A]