3GBA Membrane Protein date Feb 19, 2009
title X-Ray Structure Of Iglur5 Ligand-Binding Core (S1s2) In Comp Dysiherbaine At 1.35a Resolution
authors K.Frydenvang, P.Naur, M.Gajhede, J.S.Kastrup
compound source
Molecule: Glutamate Receptor, Ionotropic Kainate 1
Chain: A, B, C, D
Fragment: Iglur5 Ligand-Binding Core (S1s2)
Synonym: Glutamate Receptor 5, Glur-5, Glur5
Engineered: Yes
Organism_scientific: Rattus Norvegicus
Organism_common: Rat
Organism_taxid: 10116
Gene: Glur5, Grik1
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Origami 2
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-28a(+)
symmetry Space Group: P 1
R_factor 0.165 R_Free 0.193
crystal
cell
length a length b length c angle alpha angle beta angle gamma
44.872 66.902 90.342 92.69 94.66 100.82
method X-Ray Diffractionresolution 1.35 Å
ligand CL, DYH, GOL, SO4 enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, D, C, B


Primary referenceFull domain closure of the ligand-binding core of the ionotropic glutamate receptor iGluR5 induced by the high affinity agonist dysiherbaine and the functional antagonist 8,9-dideoxyneodysiherbaine., Frydenvang K, Lash LL, Naur P, Postila PA, Pickering DS, Smith CM, Gajhede M, Sasaki M, Sakai R, Pentikainen OT, Swanson GT, Kastrup JS, J Biol Chem. 2009 May 22;284(21):14219-29. Epub 2009 Mar 18. PMID:19297335
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (384 Kb) [Save to disk]
  • Biological Unit Coordinates (3gba.pdb1.gz) 98 Kb
  • Biological Unit Coordinates (3gba.pdb2.gz) 98 Kb
  • Biological Unit Coordinates (3gba.pdb3.gz) 96 Kb
  • Biological Unit Coordinates (3gba.pdb4.gz) 96 Kb
  • LPC: Ligand-Protein Contacts for 3GBA
  • CSU: Contacts of Structural Units for 3GBA
  • Likely Quarternary Molecular Structure file(s) for 3GBA
  • Structure Factors (9436 Kb)
  • Retrieve 3GBA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3GBA from S2C, [Save to disk]
  • Re-refined 3gba structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3GBA in 3D
  • Proteopedia, because life has more than 2D.
  • On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure.
  • On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.
  • Visual 3D analysis of 3GBA
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Electron Density related parameters from EDS Electron Density Server, at Upsala
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 3GBA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3gba_C] [3gba_B] [3gba_A] [3gba] [3gba_D]
  • SWISS-PROT database: [P22756]
  • Belongs to the glutamate-gated ion channel (gic) family of neurotransmitter receptors according to TCDB.
  • Domain organization of [GRIK1_RAT] by SWISSPFAM
  • Domains found in 3GBA: [Lig_chan-Glu_bd] [PBPb] [PBPe ] by SMART
  • Other resources with information on 3GBA
  • Community annotation for 3GBA at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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