9PKY | pdb_00009pky

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000 nM ivermectin

PDB DOI: https://doi.org/10.2210/pdb9PKY/pdb
EM Map EMD-71707: EMDB EMDataResource

Classification: TRANSPORT PROTEIN
Organism(s): Danio rerio
Expression System: Spodoptera aff. frugiperda 1 BOLD-2017
Mutation(s): No

Deposited: 2025-07-14 Released: 2026-01-07
Deposition Author(s): Gibbs, E., Chakrapani, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.89 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

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 2000 nM ivermectin

Gibbs, E., Chakrapani, S.

To be published.

Macromolecule Content

Total Structure Weight: 283.35 kDa
Atom Count: 14,301
Modeled Residue Count: 1,698
Deposited Residue Count: 2,423
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor, alpha 1	A, B [auth D], C, D [auth B]	458	Danio rerio	Mutation(s): 0 Gene Names: glra1
UniProt
Find proteins for B3DHZ5 (Danio rerio) Explore B3DHZ5 Go to UniProtKB: B3DHZ5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	B3DHZ5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B [auth D] Focus chain C Focus chain D [auth B]
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor beta subunit 2	E	591	Danio rerio	Mutation(s): 0 Gene Names: glrbb, glrb2
UniProt
Find proteins for Q6DC22 (Danio rerio) Explore Q6DC22 Go to UniProtKB: Q6DC22
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q6DC22
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain E
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
IVM (Subject of Investigation/LOI) Query on IVM Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain L [auth D] SDF format, chain N [auth C] SDF format, chain Q [auth B] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain L [auth D] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth B] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain L [auth D] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth B]	H [auth A], I [auth A], L [auth D], N [auth C], Q [auth B]	(2aE,4E,5'S,6S,6'R,7S,8E,11R,13R,15S,17aR,20R,20aR,20bS)-6'-[(2S)-butan-2-yl]-20,20b-dihydroxy-5',6,8,19-tetramethyl-17 -oxo-3',4',5',6,6',10,11,14,15,17,17a,20,20a,20b-tetradecahydro-2H,7H-spiro[11,15-methanofuro[4,3,2-pq][2,6]benzodioxacy clooctadecine-13,2'-pyran]-7-yl 2,6-dideoxy-4-O-(2,6-dideoxy-3-O-methyl-alpha-L-arabino-hexopyranosyl)-3-O-methyl-alpha-L-arabino-hexopyranoside C₄₈ H₇₄ O₁₄ AZSNMRSAGSSBNP-XPNPUAGNSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth D] Focus chain N [auth C] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain L [auth D] Focus chain N [auth C] Focus chain Q [auth B]
SY9 (Subject of Investigation/LOI) Query on SY9 Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth D] SDF format, chain M [auth C] SDF format, chain P [auth C] SDF format, chain S [auth B] MOL2 format, chain G [auth A] MOL2 format, chain K [auth D] MOL2 format, chain M [auth C] MOL2 format, chain P [auth C] MOL2 format, chain S [auth B] mmCIF format, chain G [auth A] mmCIF format, chain K [auth D] mmCIF format, chain M [auth C] mmCIF format, chain P [auth C] mmCIF format, chain S [auth B]	G [auth A], K [auth D], M [auth C], P [auth C], S [auth B]	STRYCHNINE C₂₁ H₂₂ N₂ O₂ QMGVPVSNSZLJIA-FVWCLLPLSA-N		Interactions Focus chain G [auth A] Focus chain K [auth D] Focus chain M [auth C] Focus chain P [auth C] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain K [auth D] Focus chain M [auth C] Focus chain P [auth C] Focus chain S [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain J [auth D] SDF format, chain O [auth C] SDF format, chain R [auth B] SDF format, chain T [auth E] SDF format, chain U [auth E] SDF format, chain F [auth A] MOL2 format, chain J [auth D] MOL2 format, chain O [auth C] MOL2 format, chain R [auth B] MOL2 format, chain T [auth E] MOL2 format, chain U [auth E] MOL2 format, chain F [auth A] mmCIF format, chain J [auth D] mmCIF format, chain O [auth C] mmCIF format, chain R [auth B] mmCIF format, chain T [auth E] mmCIF format, chain U [auth E] mmCIF format, chain F [auth A]	F [auth A] J [auth D] O [auth C] R [auth B] T [auth E] F [auth A], J [auth D], O [auth C], R [auth B], T [auth E], U [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain J [auth D] Focus chain O [auth C] Focus chain R [auth B] Focus chain T [auth E] Focus chain U [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth D] Focus chain O [auth C] Focus chain R [auth B] Focus chain T [auth E] Focus chain U [auth E]