4DLD

Crystal structure of the GluK1 ligand-binding domain (S1S2) in complex with the antagonist (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro-4-nitrophenyl)propionic acid at 2.0 A resolution

Structural Biology Knowledgebase: 4DLD SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.186

Literature

Macromolecules
Sequence Display for 4DLD

Classification: MEMBRANE PROTEIN

Total Structure Weight: 59074.29

Macromolecule Entities
Molecule Chains Length Organism Details
Glutamate receptor, ionotropic kainate 1 A, B 257 Rattus norvegicus Fragment: GluK1 Ligand binding domain (GluK1-S1S2)
Mutation: A34G
Details: The protein crystallized is the extracellular ligand binding domain of GluK1. Transmembrane regions were genetically removed and replaced with a Gly-Thr linker.
Gene Name(s): Grik1 Glur5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
TZG
Query on TZG

A, B (S)-2-amino-3-(2-(2-carboxyethyl)-5-chloro- 4-nitrophenyl)propionic acid
C12 H13 Cl N2 O6
DRCLPFURMHGQPC-VIFPVBQESA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

B SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

B GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
TZG N/A in BindingDB
Ki: 1500 nM  BindingMOAD
Ki: 1500 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.246
  • R-Value Work: 0.186
  • Space Group: P 41 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 69.32 α = 90.00
b = 69.32 β = 90.00
c = 234.97 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-02-06
  • Released Date: 2012-10-10
  • Deposition author(s): Venskutonyte, R., Frydenvang, K., Kastrup, J.S.

Revision History

No revisions since initial release