9PZW | pdb_00009pzw

GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound state

PDB DOI: https://doi.org/10.2210/pdb9PZW/pdb
EM Map EMD-72084: EMDB EMDataResource

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

Deposited: 2025-08-11 Released: 2025-12-17
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: 3.43 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

GluN1/GluN2A in complex with 3D2 Fab, glycine and glutamate-bound state

Kim, J., Gouaux, E.

To be published.

Macromolecule Content

Total Structure Weight: 447.93 kDa
Atom Count: 27,525
Modeled Residue Count: 3,493
Deposited Residue Count: 3,970
Unique protein chains: 4

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heavy chain of GluN2A-specific monoclonal Fab fragment, termed 3D2	A [auth J], G [auth L]	141	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Light chain of GluN2A-specific monoclonal Fab fragment, termed 3D2	B [auth K], H [auth M]	131	Mus musculus	Mutation(s): 0
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	C [auth A], E [auth C]	847	Rattus norvegicus	Mutation(s): 0 Gene Names: Grin1, Nmdar1
UniProt
Find proteins for P35439 (Rattus norvegicus) Explore P35439 Go to UniProtKB: P35439
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P35439
Glycosylation
Glycosylation Sites: 6	Glycosylation Focus chain C [auth A] Focus chain E [auth C]	Go to GlyGen: P35439-1
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	D [auth B], F [auth D]	866	Rattus norvegicus	Mutation(s): 0 Gene Names: Grin2a
UniProt
Find proteins for Q00959 (Rattus norvegicus) Explore Q00959 Go to UniProtKB: Q00959
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00959
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain D [auth B] Focus chain F [auth D]	Go to GlyGen: Q00959-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain Y [auth C] SDF format, chain X [auth C] SDF format, chain W [auth C] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain T [auth C] SDF format, chain R [auth B] SDF format, chain Q [auth B] SDF format, chain P [auth B] SDF format, chain O [auth B] SDF format, chain M [auth A] SDF format, chain L [auth A] SDF format, chain K [auth A] SDF format, chain J [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain Y [auth C] MOL2 format, chain X [auth C] MOL2 format, chain W [auth C] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain T [auth C] MOL2 format, chain R [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain P [auth B] MOL2 format, chain O [auth B] MOL2 format, chain M [auth A] MOL2 format, chain L [auth A] MOL2 format, chain K [auth A] MOL2 format, chain J [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain Y [auth C] mmCIF format, chain X [auth C] mmCIF format, chain W [auth C] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain T [auth C] mmCIF format, chain R [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain P [auth B] mmCIF format, chain O [auth B] mmCIF format, chain M [auth A] mmCIF format, chain L [auth A] mmCIF format, chain K [auth A] mmCIF format, chain J [auth A] mmCIF format, chain BA [auth D] mmCIF format, chain AA [auth D]	AA [auth D] BA [auth D] J [auth A] K [auth A] L [auth A] AA [auth D], BA [auth D], J [auth A], K [auth A], L [auth A], M [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], T [auth C], U [auth C], V [auth C], W [auth C], X [auth C], Y [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain L [auth A] Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain T [auth C] Focus chain U [auth C] Focus chain V [auth C] Focus chain W [auth C] Focus chain X [auth C] Focus chain Y [auth C]
GLU (Subject of Investigation/LOI) Query on GLU Download Ideal Coordinates CCD File SDF format, chain Z [auth D] SDF format, chain N [auth B] MOL2 format, chain Z [auth D] MOL2 format, chain N [auth B] mmCIF format, chain Z [auth D] mmCIF format, chain N [auth B]	N [auth B], Z [auth D]	GLUTAMIC ACID C₅ H₉ N O₄ WHUUTDBJXJRKMK-VKHMYHEASA-N		Interactions Focus chain N [auth B] Focus chain Z [auth D] Interactions & Density Focus chain N [auth B] Focus chain Z [auth D]
GLY (Subject of Investigation/LOI) Query on GLY Download Ideal Coordinates CCD File SDF format, chain S [auth C] SDF format, chain I [auth A] MOL2 format, chain S [auth C] MOL2 format, chain I [auth A] mmCIF format, chain S [auth C] mmCIF format, chain I [auth A]	I [auth A], S [auth C]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain S [auth C] Interactions & Density Focus chain I [auth A] Focus chain S [auth C]