6E7W

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115

PDB DOI: https://doi.org/10.2210/pdb6E7W/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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.232
R-Value Work: 0.190
R-Value Observed: 0.192

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 of the entry. See complete history.

Literature

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

Regan, M.C., Furukawa, H.

(2019) Nat Commun 10: 321

Macromolecule Content

Total Structure Weight: 172.95 kDa
Atom Count: 11,315
Modelled Residue Count: 1,436
Deposited Residue Count: 1,496
Unique protein chains: 2

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	A0A1L8F5J9
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain C
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q00960
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain B Focus chain D	Go to GlyGen: Q00960-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HXM (Subject of Investigation/LOI) Query on HXM Download Ideal Coordinates CCD File SDF format, chain M [auth B] SDF format, chain Y [auth D] MOL2 format, chain M [auth B] MOL2 format, chain Y [auth D] mmCIF format, chain M [auth B] mmCIF format, chain Y [auth D]	M [auth B], Y [auth D]	N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propan-2-yl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide C₂₁ H₂₈ Cl₂ N₂ O₄ S WOHKJBQMRNLVHV-SFHVURJKSA-N		Interactions Focus chain M [auth B] Focus chain Y [auth D] Interactions & Density Focus chain M [auth B] Focus chain Y [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] SDF format, chain R [auth C] SDF format, chain S [auth C] SDF format, chain T [auth C] SDF format, chain X [auth D] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B] MOL2 format, chain R [auth C] MOL2 format, chain S [auth C] MOL2 format, chain T [auth C] MOL2 format, chain X [auth D] mmCIF format, chain F [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth B] mmCIF format, chain R [auth C] mmCIF format, chain S [auth C] mmCIF format, chain T [auth C] mmCIF format, chain X [auth D]	F [auth A] G [auth A] K [auth B] L [auth B] R [auth C] F [auth A], G [auth A], K [auth B], L [auth B], R [auth C], S [auth C], T [auth C], X [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth B] Focus chain R [auth C] Focus chain S [auth C] Focus chain T [auth C] Focus chain X [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain AA [auth D] SDF format, chain BA [auth D] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain N [auth B] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth C] SDF format, chain W [auth C] SDF format, chain Z [auth D] MOL2 format, chain AA [auth D] MOL2 format, chain BA [auth D] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain N [auth B] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth C] MOL2 format, chain W [auth C] MOL2 format, chain Z [auth D] mmCIF format, chain AA [auth D] mmCIF format, chain BA [auth D] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain N [auth B] mmCIF format, chain O [auth B] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth C] mmCIF format, chain W [auth C] mmCIF format, chain Z [auth D]	AA [auth D] BA [auth D] I [auth A] J [auth A] N [auth B] AA [auth D], BA [auth D], I [auth A], J [auth A], N [auth B], O [auth B], P [auth B], Q [auth B], V [auth C], W [auth C], Z [auth D]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain I [auth A] Focus chain J [auth A] Focus chain N [auth B] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain V [auth C] Focus chain W [auth C] Focus chain Z [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain U [auth C] MOL2 format, chain H [auth A] MOL2 format, chain U [auth C] mmCIF format, chain H [auth A] mmCIF format, chain U [auth C]	H [auth A], U [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain U [auth C] Interactions & Density Focus chain H [auth A] Focus chain U [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.67 Å
R-Value Free: 0.232
R-Value Work: 0.190
R-Value Observed: 0.192
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 268.131	α = 90
b = 59.59	β = 116.62
c = 145.495	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-01-30

Deposition Author(s):

Regan, M.C.

Furukawa, H.

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 (Full details and data files)

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
Version 2.2: 2024-11-06
Changes: Structure summary

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Help and Resources

6E7W

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-115

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

Entity ID: 1

UniProt

Entity Groups

Glycosylation

Sequence Annotations

Expand

Entity ID: 2