2F34

Crystal Structure of the GluR5 Ligand Binding Core Dimer with UBP310 At 1.74 Angstroms Resolution

Structural Biology Knowledgebase: 2F34 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.181

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2F34

Classification: MEMBRANE PROTEIN

Total Structure Weight: 59677.61

Macromolecule Entities
Molecule Chains Length Organism Details
GLUTAMATE RECEPTOR, IONOTROPIC KAINATE 1 A, B 258 Rattus norvegicus Fragment: GluR5 ligand binding core (sequence database 446-559 and 682-821)
Mutation: E258S
Gene Name(s): Grik1 Glur5
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A, B (S)-1-(2-AMINO-2-CARBOXYETHYL)-3(2-CARBOXYTHIOPHENE- 3-YL-METHYL)-5-METHYLPYRIMIDINE-2,4-DIONE
C14 H15 N3 O6 S
ZTAZUCRXCRXNSU-VIFPVBQESA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1PE
Query on 1PE

A, B PENTAETHYLENE GLYCOL
PEG400 (Synonym)
C10 H22 O6
JLFNLZLINWHATN-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CL
Query on CL

A, B CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
UBA IC50: >100000 nM (88) BindingDB
Kd: 18 nM (97) BindingDB
Ki: 23 nM (86) BindingDB

Kd: 130 nM  BindingMOAD
Kd: 130 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.74 Å
  • R-Value Free: 0.211
  • R-Value Work: 0.181
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.70 α = 90.00
b = 97.95 β = 90.00
c = 129.13 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-18
  • Released Date: 2006-04-04
  • Deposition author(s): Mayer, M.L.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values