6E7R | pdb_00006e7r

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)

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.218 (Depositor), 0.220 (DCC)
R-Value Work:
0.189 (Depositor), 0.200 (DCC)
R-Value Observed:
0.190 (Depositor)

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., 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

Macromolecule Content

Total Structure Weight: 172.89 kDa
Atom Count: 11,522
Modeled 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

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	Interactions Focus chain E Interactions & Density Focus chain E
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	Interactions Focus chain F Interactions & Density Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HYS (Subject of Investigation/LOI) Query on HYS Download Ideal Coordinates CCD File SDF format, chain X [auth D] SDF format, chain N [auth B] MOL2 format, chain X [auth D] MOL2 format, chain N [auth B] mmCIF format, chain X [auth D] mmCIF format, chain N [auth B]	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		Interactions Focus chain N [auth B] Focus chain X [auth D] Interactions & Density Focus chain N [auth B] Focus chain X [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain L [auth B] SDF format, chain W [auth D] SDF format, chain S [auth C] SDF format, chain M [auth B] SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain L [auth B] MOL2 format, chain W [auth D] MOL2 format, chain S [auth C] MOL2 format, chain M [auth B] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain L [auth B] mmCIF format, chain W [auth D] mmCIF format, chain S [auth C] mmCIF format, chain M [auth B] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A] H [auth A] L [auth B] M [auth B] S [auth C] 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		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain S [auth C] Focus chain W [auth D]
CL Query on CL Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth B] SDF format, chain Y [auth D] SDF format, chain Z [auth D] SDF format, chain V [auth C] SDF format, chain U [auth C] SDF format, chain R [auth B] SDF format, chain P [auth B] SDF format, chain K [auth A] SDF format, chain BA [auth D] SDF format, chain AA [auth D] MOL2 format, chain J [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain Y [auth D] MOL2 format, chain Z [auth D] MOL2 format, chain V [auth C] MOL2 format, chain U [auth C] MOL2 format, chain R [auth B] MOL2 format, chain P [auth B] MOL2 format, chain K [auth A] MOL2 format, chain BA [auth D] MOL2 format, chain AA [auth D] mmCIF format, chain J [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain Y [auth D] mmCIF format, chain Z [auth D] mmCIF format, chain V [auth C] mmCIF format, chain U [auth C] mmCIF format, chain R [auth B] mmCIF format, chain P [auth B] mmCIF format, chain K [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] O [auth B] 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		Interactions Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D] Interactions & Density Focus chain AA [auth D] Focus chain BA [auth D] Focus chain J [auth A] Focus chain K [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain Q [auth B] Focus chain R [auth B] Focus chain U [auth C] Focus chain V [auth C] Focus chain Y [auth D] Focus chain Z [auth D]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain T [auth C] MOL2 format, chain I [auth A] MOL2 format, chain T [auth C] mmCIF format, chain I [auth A] mmCIF format, chain T [auth C]	I [auth A], T [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain I [auth A] Focus chain T [auth C] Interactions & Density Focus chain I [auth A] Focus chain T [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.218 (Depositor), 0.220 (DCC)
R-Value Work: 0.189 (Depositor), 0.200 (DCC)
R-Value Observed: 0.190 (Depositor)

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

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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: 2024-11-20
Changes: Structure summary

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Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 6E7R | pdb_00006e7r

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

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