6E7R

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-4

• PDB DOI: https://doi.org/10.2210/pdb6E7R/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Xenopus laevis, Rattus norvegicus
• Expression System: Trichoplusia ni
• Mutation(s): Yes 
• Membrane Protein: Yes  mpstruc


• Deposited: 2018-07-27 Released: 2019-01-30 
• Deposition Author(s): Regan, M.C., Furukawa, H.
• Funding Organization(s): National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS), National Institutes of Health/National Institute of Mental Health (NIH/NIMH)

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 

Starting Model: experimental

Literature

Structural elements of a pH-sensitive inhibitor binding site in NMDA receptors

Regan, M.C., Zhu, Z., Yuan, H., Myers, S.J., Menaldino, D.S., Tahirovic, Y.A., Liotta, D.C., Traynelis, S.F., Furukawa, H.

(2019) Nat Commun 10: 321

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content

• Total Structure Weight: 172.89 kDa 
• Atom Count: 11,522 
• Modelled Residue Count: 1,436 
• Deposited Residue Count: 1,496 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 1	A, C	385	Xenopus laevis	Mutation(s): 2  Gene Names: grin1 Membrane Entity: Yes
UniProt
Find proteins for A0A1L8F5J9 (Xenopus laevis) Explore A0A1L8F5J9  Go to UniProtKB:  A0A1L8F5J9
Glycosylation
Glycosylation Sites: 3

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor ionotropic, NMDA 2B	B, D	363	Rattus norvegicus	Mutation(s): 1  Gene Names: Grin2b Membrane Entity: Yes
UniProt
Find proteins for Q00960 (Rattus norvegicus) Explore Q00960  Go to UniProtKB:  Q00960
Glycosylation
Glycosylation Sites: 2		Go to GlyGen: Q00960-1

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G22768VO GlyCosmos:  G22768VO GlyGen:  G22768VO

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HYS (Subject of Investigation/LOI)	N [auth B], X [auth D]	N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl]amino}-2-hydroxypropoxy]phenyl}methanesulfonamide C18 H22 Cl2 N2 O4 S GEFDXUZHLNJUMR-HNNXBMFYSA-N
NAG	G [auth A], H [auth A], L [auth B], M [auth B], S [auth C], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CL	AA [auth D], BA [auth D], J [auth A], K [auth A], O [auth B], P [auth B], Q [auth B], R [auth B], U [auth C], V [auth C], Y [auth D], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
NA	I [auth A], T [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.10 Å
• R-Value Free: 0.218 
• R-Value Work: 0.189 
• R-Value Observed: 0.190 
• Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 267.953	α = 90
b = 59.898	β = 116.69
c = 145.286	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
DENZO	data reduction
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2019-01-30 
Deposition Author(s): Regan, M.C., Furukawa, H.

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Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)	United States	F32NS093753
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)	United States	R01MH085926

Revision History  

• Version 1.0: 2019-01-30
  Type: Initial release
  
• Version 1.1: 2019-11-27
  Changes: Author supporting evidence
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-10-11
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary