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 
- 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 
- R-Value Work: 0.189 
- R-Value Observed: 0.190 
This is version 2.1 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
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Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate receptor ionotropic, NMDA 1 | 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 | ||||
Sequence AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Glutamate receptor ionotropic, NMDA 2B | 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 | ||||
Sequence AnnotationsExpand | |||||
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Oligosaccharides
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 |
Small Molecules
Ligands 4 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
HYS (Subject of Investigation/LOI) Query on HYS | 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 Query on NAG | G [auth A] H [auth A] L [auth B] M [auth B] S [auth C] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
CL Query on CL | AA [auth D] BA [auth D] J [auth A] K [auth A] O [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M | |||
NA Query on 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 Name | Purpose |
---|---|
REFMAC | refinement |
DENZO | data reduction |
HKL-2000 | data scaling |
PDB_EXTRACT | data extraction |
PHASER | phasing |
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