1MY4

crystal structure of glutamate receptor ligand-binding core in complex with iodo-willardiine in the Zn crystal form

Structural Biology Knowledgebase: 1MY4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.213

Literature

Macromolecules
Sequence Display for 1MY4

Classification: membrane protein

Total Structure Weight: 88967.72

Macromolecule Entities
Molecule Chains Length Organism Details
GLUTAMATE RECEPTOR 2 A, B, C 263 Rattus norvegicus Fragment: LIGAND BINDING CORE (S1S2J)
Gene Name(s): Gria2 Glur2
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B, C 2-AMINO-3-(5-IODO-2,4-DIOXO-3,4-DIHYDRO-2H- PYRIMIDIN-1-YL)-PROPIONIC ACID
IODO-WILLARDIINE (Synonym)
C7 H8 I N3 O4
AXXYLTBQIQBTES-BYPYZUCNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A, B, C ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IWD Ki: 105 - 976 nM (88 - 99) BindingDB

N/A in BindingMoad
Ki: 105 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.9 Å
  • R-Value Free: 0.262
  • R-Value Work: 0.213
  • Space Group: P 21 21 2

Unit Cell:

Length (Å) Angle (°)
a = 113.84 α = 90.00
b = 163.80 β = 90.00
c = 48.01 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2002-10-03
  • Released Date: 2003-06-10
  • Deposition author(s): Jin, R., Gouaux, E.

Revision History

  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4