9NYZ | pdb_00009nyz

Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with UCM-101

• PDB DOI: https://doi.org/10.2210/pdb9NYZ/pdb

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


• Deposited: 2025-03-30 Released: 2025-10-29 
• Deposition Author(s): Lotti, J.S., Syrenne, J.T., Yates-Hansen, C.K., McClelland, L.J., Hansen, K.B.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free: 
  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 
  0.169 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of DCKA/glutamate-bound GluN1/GluN2A agonist binding domains with UCM-101

Hansen, K.B.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 65.94 kDa 
• Atom Count: 5,147 
• Modeled Residue Count: 566 
• Deposited Residue Count: 575 
• Unique protein chains: 2

Macromolecules

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 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
A1B7E (Subject of Investigation/LOI)	D [auth B]	N-(cyclohexylmethyl)-2-[(5-{[(1R)-1-phenylpropyl]amino}-1,3,4-thiadiazol-2-yl)sulfanyl]acetamide C20 H28 N4 O S2 HTAOPHYTYWYDAU-QGZVFWFLSA-N
DK1 (Subject of Investigation/LOI)	C [auth A]	5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID C10 H5 Cl2 N O3 BGKFPRIGXAVYNX-UHFFFAOYSA-N
GLU (Subject of Investigation/LOI)	E [auth B]	GLUTAMIC ACID C5 H9 N O4 WHUUTDBJXJRKMK-VKHMYHEASA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.71 Å
• R-Value Free:  0.202 (Depositor), 0.202 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.168 (DCC) 
• R-Value Observed: 0.169 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 54.474	α = 90
b = 88.329	β = 90
c = 137.273	γ = 90

Software Package:

Software Name	Purpose
autoPROC	data processing
PHASER	phasing
PHENIX	refinement
Coot	model building
autoPROC	data reduction
autoPROC	data scaling

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2025-10-29 
Deposition Author(s): Lotti, J.S., Syrenne, J.T., Yates-Hansen, C.K., McClelland, L.J., Hansen, K.B.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	R01NS097536
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	P30GM140963

Revision History  

• Version 1.0: 2025-10-29
  Type: Initial release