9Y96 | pdb_00009y96

Homomeric Glycine Receptor alpha2 with 1 mM Glycine in a Closed State

PDB DOI: https://doi.org/10.2210/pdb9Y96/pdb
EM Map EMD-72690: EMDB EMDataResource

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

Deposited: 2025-09-13 Released: 2026-03-18
Deposition Author(s): Klemm, E., Gibbs, E., Chakrapani, S.
Funding Organization(s): National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.36 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

Human GlyRa2 Pore Dynamics in Gating and Inhibition

Klemm, E., Gibbs, E., Stauffer, M., Mohapatra, D., Meyer, C., Chakrapani, S.

(2026) Structure

DOI: https://doi.org/10.1016/j.str.2026.02.013

Macromolecule Content

Total Structure Weight: 271.5 kDa
Atom Count: 14,165
Modeled Residue Count: 1,730
Deposited Residue Count: 2,330
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-2	A, B, C, D, E	466	Homo sapiens	Mutation(s): 0 Gene Names: GLRA2
UniProt & NIH Common Fund Data Resources
Find proteins for P23416 (Homo sapiens) Explore P23416 Go to UniProtKB: P23416
PHAROS: P23416 GTEx: ENSG00000101958
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23416
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E	Go to GlyGen: P23416-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain S [auth E] SDF format, chain T [auth E] SDF format, chain J [auth B] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] MOL2 format, chain T [auth E] MOL2 format, chain J [auth B] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain I [auth B] mmCIF format, chain L [auth C] mmCIF format, chain M [auth C] mmCIF format, chain O [auth D] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E] mmCIF format, chain T [auth E] mmCIF format, chain J [auth B]	F [auth A] G [auth A] I [auth B] J [auth B] L [auth C] F [auth A], G [auth A], I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D], S [auth E], 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 G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain S [auth E] Focus chain T [auth E]
GLY (Subject of Investigation/LOI) Query on GLY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain R [auth E] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain R [auth E] mmCIF format, chain H [auth A] mmCIF format, chain K [auth B] mmCIF format, chain N [auth C] mmCIF format, chain Q [auth D] mmCIF format, chain R [auth E]	H [auth A], K [auth B], N [auth C], Q [auth D], R [auth E]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain R [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 3.36 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.19.2_4158
RECONSTRUCTION	PHENIX	1.19.2_4158

Structure Validation

View Full Validation Report

Entry History & Funding Information

Deposition Data

Released Date: 2026-03-18

Deposition Author(s):

Klemm, E.

Gibbs, E.

Chakrapani, S.

Funding Organization	Location	Grant Number
National Institutes of Health/Eunice Kennedy Shriver National Institute of Child Health & Human Development (NIH/NICHD)	United States	1F30HD114399-01
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	2R35 GM134896-06
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	GM152319