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

Literature

Macromolecules
Sequence Display for 1PB8

Classification: LIGAND BINDING PROTEIN

Total Structure Weight: 33432.13

Macromolecule Entities
Molecule Chains Length Organism Details
N-methyl-D-aspartate Receptor Subunit 1 A 292 Rattus norvegicus Fragment: Ligand Binding Core
Gene Name(s): Grin1 Nmdar1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
DSN
Query on DSN

A D-SERINE
C3 H7 N O3
MTCFGRXMJLQNBG-UWTATZPHSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DSN IC50: 670 nM (99) BindingDB

Ki: 7020 nM  BindingMOAD
Ki: 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 = 41.46 α = 90.00
b = 73.06 β = 90.00
c = 96.89 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-05-14
  • Released Date: 2003-06-24
  • Deposition author(s): Furukawa, H., Gouaux, E.

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