2PBW

Crystal Structure of the Ligand-Binding Core of iGluR5 in Complex with the Partial agonist Domoic Acid at 2.5 A Resolution

Structural Biology Knowledgebase: 2PBW SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.209

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2PBW

Classification: MEMBRANE PROTEIN

Total Structure Weight: 58839.96

Macromolecule Entities
Molecule Chains Length Organism Details
Glutamate receptor, ionotropic kainate 1 A, B 257 Rattus norvegicus Mutation: A34G
Gene Name(s): Grik1 Glur5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B (2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY- 1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID
3S, (Synonym)
C15 H21 N O6
VZFRNCSOCOPNDB-AOKDLOFSSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
DOQ N/A in BindingDB
Ki: 5.56 nM  BindingMOAD
Ki: 5.56 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.248
  • R-Value Work: 0.209
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 70.86 α = 90.00
b = 70.86 β = 90.00
c = 233.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-03-29
  • Released Date: 2007-07-03
  • Deposition author(s): Hald, H., Naur, P., Gajhede, M., Kastrup, J.S.

Revision History

  • 2012-06-13
    Type: Other | Details: update matrix records
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4