9OFM | pdb_00009ofm

GluN1/GluN3A in complex with glycine, LBD focused, in desensitized conformation

PDB DOI: https://doi.org/10.2210/pdb9OFM/pdb
EM Map EMD-70437: EMDB EMDataResource

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

Deposited: 2025-04-29 Released: 2026-08-26
Deposition Author(s): Kim, J., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 4.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 9OFM

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

Literature

GluN1/GluN3A in complex with glycine, LBD focused, in desensitized conformation

Kim, J., Gouaux, E.

To be published.

Macromolecule Content

Total Structure Weight: 414.52 kDa
Atom Count: 8,308
Modeled Residue Count: 1,128
Deposited Residue Count: 3,680
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Isoform E of Glutamate receptor ionotropic, NMDA 1	A, C	870	Rattus norvegicus	Mutation(s): 0 Gene Names: Grin1, Nmdar1
UniProt
Find proteins for P35439 (Rattus norvegicus) Go to UniProtKB: P35439
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35439-5
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain C	Go to GlyGen: P35439-1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 3A	B [auth D], D [auth B]	970	Rattus norvegicus	Mutation(s): 0 Gene Names: Grin3a
UniProt
Find proteins for Q9R1M7 (Rattus norvegicus) Explore Q9R1M7 Go to UniProtKB: Q9R1M7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q9R1M7
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B [auth D] Focus chain D [auth B]	Go to GlyGen: Q9R1M7-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG (Subject of Investigation/LOI) Query on NAG Download:Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain F [auth A] SDF format, chain G [auth D] SDF format, chain H [auth D] SDF format, chain I [auth D] SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain F [auth A] MOL2 format, chain G [auth D] MOL2 format, chain H [auth D] MOL2 format, chain I [auth D] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain F [auth A] mmCIF format, chain G [auth D] mmCIF format, chain H [auth D] mmCIF format, chain I [auth D] mmCIF format, chain J [auth C] mmCIF format, chain K [auth C] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain N [auth B]	E [auth A] F [auth A] G [auth D] H [auth D] I [auth D] E [auth A], F [auth A], G [auth D], H [auth D], I [auth D], J [auth C], K [auth C], L [auth B], M [auth B], N [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain F [auth A] Focus chain G [auth D] Focus chain H [auth D] Focus chain I [auth D] Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth B] Focus chain M [auth B] Focus chain N [auth B]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 4.04 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

EM Software:

Task	Software Package	Version
MODEL REFINEMENT	PHENIX	1.20.1_4487
RECONSTRUCTION	cryoSPARC	4.4

Structure Validation

View Full Validation Report

View more in-depth experimental data

Entry History

& Funding Information

Deposition Data

Released Date: 2026-08-26

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	--

Revision History (Full details and data files)

Version 1.0: 2026-08-26
Type: Initial release

RCSB PDB is hosted by

RCSB PDB is a member of

RCSB Partners
Nucleic Acid Knowledgebase

CoreTrustSeal

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.