1PB8

CRYSTAL STRUCTURE OF THE NR1 LIGAND BINDING CORE IN COMPLEX WITH D-SERINE AT 1.45 ANGSTROMS RESOLUTION


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

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

  • DOI: 10.1093/emboj/cdg303
  • Primary Citation of Related Structures:  1PB7, 1PB9, 1PBQ
  • 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 ...

    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.


    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
MoleculeChainsSequence LengthOrganismDetails
N-methyl-D-aspartate Receptor Subunit 1
A
292Rattus norvegicusGene Names: Grin1 (Nmdar1)
Find proteins for P35439 (Rattus norvegicus)
Go to UniProtKB:  P35439
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
DSN
Query on DSN

Download SDF File 
Download CCD File 
A
D-SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-UWTATZPHSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
DSNIC50: 670 nM (99) BINDINGDB
DSNKi: 7020 nM BINDINGMOAD
DSNKi: 7020 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.45 Å
  • R-Value Free: 0.226 
  • R-Value Work: 0.204 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 41.460α = 90.00
b = 73.060β = 90.00
c = 96.890γ = 90.00
Software Package:
Software NamePurpose
CNSphasing
DENZOdata reduction
SCALEPACKdata scaling
CNSrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2003-06-24
    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: 2017-07-26
    Type: Refinement description, Source and taxonomy