9PKZ | pdb_00009pkz

Alpha1/Beta Heteromeric Glycine receptor in the presence of 0.200 mM strychnine and 0.02 mM ivermectin

PDB DOI: https://doi.org/10.2210/pdb9PKZ/pdb
EM Map EMD-71708: 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

Validation slider image for 9PKZ

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 0.02 mM ivermectin

Gibbs, E., Chakrapani, S.

To be published.

Macromolecule Content

Total Structure Weight: 283.12 kDa
Atom Count: 14,429
Modeled Residue Count: 1,714
Deposited Residue Count: 2,423
Unique protein chains: 2

Macromolecules

Find similar proteins by:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% 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:

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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q6DC22
Glycosylation
Glycosylation Sites: 1	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 S [auth B] SDF format, chain O [auth C] SDF format, chain L [auth D] SDF format, chain I [auth A] SDF format, chain G [auth A] MOL2 format, chain S [auth B] MOL2 format, chain O [auth C] MOL2 format, chain L [auth D] MOL2 format, chain I [auth A] MOL2 format, chain G [auth A] mmCIF format, chain S [auth B] mmCIF format, chain O [auth C] mmCIF format, chain L [auth D] mmCIF format, chain I [auth A] mmCIF format, chain G [auth A]	G [auth A], I [auth A], L [auth D], O [auth C], S [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 G [auth A] Focus chain I [auth A] Focus chain L [auth D] Focus chain O [auth C] Focus chain S [auth B] Interactions & Density Focus chain G [auth A] Focus chain I [auth A] Focus chain L [auth D] Focus chain O [auth C] Focus chain S [auth B]
SY9 (Subject of Investigation/LOI) Query on SY9 Download:Ideal Coordinates CCD File SDF format, chain Q [auth B] SDF format, chain P [auth C] SDF format, chain M [auth D] SDF format, chain K [auth D] SDF format, chain H [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth C] MOL2 format, chain M [auth D] MOL2 format, chain K [auth D] MOL2 format, chain H [auth A] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth C] mmCIF format, chain M [auth D] mmCIF format, chain K [auth D] mmCIF format, chain H [auth A]	H [auth A], K [auth D], M [auth D], P [auth C], Q [auth B]	STRYCHNINE C₂₁ H₂₂ N₂ O₂ QMGVPVSNSZLJIA-FVWCLLPLSA-N		Interactions Focus chain H [auth A] Focus chain K [auth D] Focus chain M [auth D] Focus chain P [auth C] Focus chain Q [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth D] Focus chain M [auth D] Focus chain P [auth C] Focus chain Q [auth B]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain T [auth E] SDF format, chain R [auth B] SDF format, chain N [auth C] SDF format, chain J [auth D] SDF format, chain F [auth A] MOL2 format, chain T [auth E] MOL2 format, chain R [auth B] MOL2 format, chain N [auth C] MOL2 format, chain J [auth D] MOL2 format, chain F [auth A] mmCIF format, chain T [auth E] mmCIF format, chain R [auth B] mmCIF format, chain N [auth C] mmCIF format, chain J [auth D] mmCIF format, chain F [auth A]	F [auth A], J [auth D], N [auth C], R [auth B], T [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 N [auth C] Focus chain R [auth B] Focus chain T [auth E] Interactions & Density Focus chain F [auth A] Focus chain J [auth D] Focus chain N [auth C] Focus chain R [auth B] Focus chain T [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.89 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	RELION

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2026-01-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-01-07
Type: Initial release

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.