2OJT

Structure and mechanism of kainate receptor modulation by anions

Structural Biology Knowledgebase: 2OJT SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.190

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2OJT

Classification: MEMBRANE PROTEIN

Total Structure Weight: 59766.51

Macromolecule Entities
Molecule Chains Length Organism Details
Glutamate receptor, ionotropic kainate 1 A, B 258 Rattus norvegicus Mutation: A34G, 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)
BR
Query on BR

A, B BROMIDE ION
Br
CPELXLSAUQHCOX-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

N/A in BindingMoad
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.233
  • R-Value Work: 0.190
  • Space Group: C 2 2 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 97.60 α = 90.00
b = 97.73 β = 90.00
c = 128.69 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2007-01-14
  • Released Date: 2007-04-03
  • 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: Refinement description | Details: Fixed TLS group
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4