Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 67196.18 
• Atom Count: 4102 
• Residue Count: 584 
• Unique protein chains: 1

1PBQ

CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH 5,7-DICHLOROKYNURENIC ACID (DCKA) AT 1.90 ANGSTROMS RESOLUTION

• DOI: 10.2210/pdb1PBQ/pdb

• Classification: LIGAND BINDING PROTEIN
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli


• Deposited: 2003-05-14 Released: 2003-07-29 
• Deposition Author(s): Furukawa, H., Gouaux, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.270 
• R-Value Work: 0.231 

Literature

Mechanisms of activation, inhibition and specificity: crystal structures of the NMDA receptor NR1 ligand-binding core

Furukawa, H., Gouaux, E.

(2003) Embo J. 22: 2873-2885

• PubMed: 12805203 
• DOI: 10.1093/emboj/cdg303
• Primary Citation of Related Structures:  
  1PB9, 1PB8, 1PB7
• Also Cited By: 4KFQ


• PubMed Abstract: 
  

Excitatory neurotransmission mediated by the N-methyl-D-aspartate subtype of ionotropic glutamate receptors is fundamental to the development and function of the mammalian central nervous system. NMDA receptors require both glycine and glutamate for activation with NR1 and NR2 forming glycine and glutamate sites, respectively. Mechanisms to describe agonist and antagonist binding, and activation and desensitization of NMDA receptors have been hampered by the lack of high-resolution structures. Here, we describe the cocrystal structures of the NR1 S1S2 ligand-binding core with the agonists glycine and D-serine (DS), the partial agonist D-cycloserine (DCS) and the antagonist 5,7-dichlorokynurenic acid (DCKA). The cleft of the S1S2 'clamshell' is open in the presence of the antagonist DCKA and closed in the glycine, DS and DCS complexes. In addition, the NR1 S1S2 structure reveals the fold and interactions of loop 1, a cysteine-rich region implicated in intersubunit allostery.

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Organizational Affiliation: 

Department of Biochemistry and Molecular Biophysics, Columbia University, 650 West 168th Street, New York, NY 10032, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
N-methyl-D-aspartate Receptor Subunit 1	A, B	292	Rattus norvegicus	Mutation(s): 0  Gene Names: Grin1 (Nmdar1)
Find proteins for P35439 (Rattus norvegicus) Go to UniProtKB:  P35439

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
DK1	A, B	5,7-DICHLORO-4-HYDROXYQUINOLINE-2-CARBOXYLIC ACID DCKA, 5,7-DICHLOROKYNURENIC ACID C10 H5 Cl2 N O3 BGKFPRIGXAVYNX-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
DK1	Ki: 540 nM BINDINGMOAD
DK1	Ki: 540 nM PDBBIND

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.9 Å
• R-Value Free: 0.270 
• R-Value Work: 0.231 
• Space Group: C 1 2 1

Unit Cell:

Length (Å)	Angle (°)
a = 85.700	α = 90.00
b = 65.300	β = 98.10
c = 124.300	γ = 90.00

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
AMoRE	phasing
CNS	refinement
DENZO	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2003-05-14 
• Released Date: 2003-07-29 
• Deposition Author(s): Furukawa, H., Gouaux, E.

Revision History 

• Version 1.0: 2003-07-29
  Type: Initial release
• Version 1.1: 2008-04-29
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Version format compliance
• Version 1.3: 2017-08-16
  Type: Source and taxonomy