5TPW

Crystal structure of amino terminal domains of the NMDA receptor subunit GluN1 and GluN2A in complex with zinc at the GluN2A


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.909 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Molecular Basis for Subtype Specificity and High-Affinity Zinc Inhibition in the GluN1-GluN2A NMDA Receptor Amino-Terminal Domain.

Romero-Hernandez, A.Simorowski, N.Karakas, E.Furukawa, H.

(2016) Neuron 92: 1324-1336


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
NMDA glutamate receptor subunit
A
389Xenopus laevisMutation(s): 2 
Gene Names: grin1
Find proteins for A0A1L8F5J9 (Xenopus laevis)
Go to UniProtKB:  A0A1L8F5J9
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Glutamate receptor ionotropic, NMDA 2A
B
360Rattus norvegicusMutation(s): 0 
Gene Names: Grin2a
Find proteins for Q00959 (Rattus norvegicus)
Go to UniProtKB:  Q00959
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FAB, HEAVY CHAIN
H
221N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FAB, LIGHT CHAIN
L
214N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
ZN
Query on ZN

Download SDF File 
Download CCD File 
B
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
SO4
Query on SO4

Download SDF File 
Download CCD File 
A, B
SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
A
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.909 Å
  • R-Value Free: 0.245 
  • R-Value Work: 0.200 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 79.560α = 90.00
b = 118.401β = 90.00
c = 155.812γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
PHASERphasing
PDB_EXTRACTdata extraction
PHENIXrefinement
HKL-2000data collection
DENZOdata reduction
HKL-2000data reduction
PHENIXmodel building

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of Mental HealthUnited StatesMH085926
National Institutes of Health/National Institute of General Medical SciencesUnited StatesGM105730

Revision History 

  • Version 1.0: 2016-12-14
    Type: Initial release
  • Version 1.1: 2017-09-20
    Type: Author supporting evidence, Refinement description
  • Version 1.2: 2018-05-16
    Type: Data collection, Database references