6E7T

Heterodimer of the GluN1b-GluN2B NMDA receptor amino-terminal domains bound to allosteric inhibitor 93-6

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

  • 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: 2.31 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 

wwPDB Validation 3D Report Full Report



Literature

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

Regan, M.C.Furukawa, H.

(2019) Nat Commun 10: 321


Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 1A, C385Xenopus laevisMutation(s): 2 
Gene Names: grin1
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Explore A0A1L8F5J9 
Go to UniProtKB:  A0A1L8F5J9
Protein Feature View
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  • Reference Sequence
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Glutamate receptor ionotropic, NMDA 2BB, D363Rattus norvegicusMutation(s): 1 
Gene Names: Grin2b
Find proteins for Q00960 (Rattus norvegicus)
Explore Q00960 
Go to UniProtKB:  Q00960
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 3
MoleculeChainsChain Length2D Diagram Glycosylation
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
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
HYY
Query on HYY

Download CCD File 
B, D
N-{4-[(2S)-3-{[2-(3,4-dichlorophenyl)ethyl](propyl)amino}-2-hydroxypropoxy]phenyl}methanesulfonamide
C21 H28 Cl2 N2 O4 S
GTHAOZQJYKITBT-SFHVURJKSA-N
 Ligand Interaction
NAG
Query on NAG

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A, B, C, D
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CL
Query on CL

Download CCD File 
A, B, C, D
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
NA
Query on NA

Download CCD File 
A, C
SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.31 Å
  • R-Value Free: 0.225 
  • R-Value Work: 0.194 
  • R-Value Observed: 0.195 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 268.594α = 90
b = 59.835β = 116.86
c = 146.015γ = 90
Software Package:
Software NamePurpose
REFMACrefinement
HKL-2000data scaling
PDB_EXTRACTdata extraction
DENZOdata reduction
PHASERphasing

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS)United StatesF32NS093753
National Institutes of Health/National Institute of Mental Health (NIH/NIMH)United StatesR01MH085926

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