6OVD | pdb_00006ovd

Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 3-ethylphenyl-ACEPC

PDB DOI: https://doi.org/10.2210/pdb6OVD/pdb

Classification: PROTEIN TRANSPORT
Organism(s): Rattus norvegicus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2019-05-07 Released: 2020-05-13
Deposition Author(s): Syrenne, J.T., Mou, T.C., Tamborini, L., Pinto, A., Sprang, S.R., Hansen, K.B.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.240 (Depositor), 0.240 (DCC)
R-Value Work:
0.194 (Depositor), 0.194 (DCC)
R-Value Observed:
0.197 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal structure of GluN1/GluN2A NMDA receptor agonist binding domains with glycine and antagonist, 3-ethylphenyl-ACEPC

Syrenne, J.T., Mou, T.C., Tamborini, L., Pinto, A., Sprang, S.R., Hansen, K.B.

To be published.

Macromolecule Content

Total Structure Weight: 65.51 kDa
Atom Count: 4,752
Modeled Residue Count: 554
Deposited Residue Count: 575
Unique protein chains: 2

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	A	292	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P35439
Sequence Annotations Expand
Reference Sequence

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| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2A	B	283	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q00959
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
N9A (Subject of Investigation/LOI) Query on N9A Download:Ideal Coordinates CCD File SDF format, chain D [auth B] MOL2 format, chain D [auth B] mmCIF format, chain D [auth B]	D [auth B]	(3S,5S)-5-[(2R)-2-amino-2-carboxyethyl]-1-(3-ethylphenyl)pyrazolidine-3-carboxylic acid C₁₅ H₂₁ N₃ O₄ LCLMUHPMEPOVIB-XQQFMLRXSA-N		Interactions Focus chain D [auth B] Interactions & Density Focus chain D [auth B]
GLY Query on GLY Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.240 (Depositor), 0.240 (DCC)
R-Value Work: 0.194 (Depositor), 0.194 (DCC)
R-Value Observed: 0.197 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.666	α = 90
b = 87.237	β = 90
c = 122.597	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2020-05-13

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P20GM103546
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS097536

Revision History (Full details and data files)

Version 1.0: 2020-05-13
Type: Initial release
Version 1.1: 2023-10-11
Changes: Data collection, Database references, Refinement description
Version 1.2: 2024-11-20
Changes: Structure summary