Brand  (β version)

PDB ID: 6YK4

Hetero Atom Contents

  The number of atoms exceeds 100,000.
  So, it can not be displayed here.

Select unit:

Select hetatm:   

close
information
centroid:
interaction residue:

Select chain:   Sequence  

Data format:   

Color scheme of protein:

Ligands
Code Name Style Show Link
CG8 (2~{S})-2-azanyl-3-[6-methyl-2,4-bis(oxidanylidene)-5,7-dihydropyrrolo[3,4-D]pyrimidin-1-yl]propanoic acid PoSSuM
CL Chloride ion PoSSuM
GOL Glycerol PoSSuM
LI Lithium ion PoSSuM
SO4 Sulfate ion PoSSuM
Non-standard Residues
Code Name Show
Glycosylation
Code Name Emphasize
Modification
Code Name Show

Structure summary

Code : 6YK4   PDBj   RCSB PDB   PDBe
Header : MEMBRANE PROTEIN
Title : Structure of the AMPA receptor GluA2o ligand-binding domain (S1S2J) in complex with the compound ( S) - 1- [2'-Amino-2'-carboxyethyl]-6-methyl-5 ,7- dihydropyrrolo[3,4-D]pyrimidin-2,4(1H,3H)-dione at resolution 1.00A
Release Data : 2020-06-03
Compound :
mol_id molecule chains synonym
1 Glutamate receptor 2,Glutamate receptor 2 A GluR-2,AMPA-selective glutamate receptor 2,GluR-B,GluR-K2,Glutamate receptor ionotropic,AMPA 2,GluA2
other_details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUA2O. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 118-119). THE SEQUENCE MATCHES DISCONTINOUSLY WITH THE REFERENCE DATABASE (UNP RESIDUES 413-527 AND 653-797, NUMBERING WITH SIGNAL PEPTIDE OF 21 AMINO ACIDS). THE TWO FIRST RESIDUES (GLY, ALA) ARE CLONING REMNANTS.
Source :
mol_id organism_scientific organism_common expression_system
1 Rattus norvegicus  (taxid:10116) Norway Rat Escherichia coli BL21(DE3)  (taxid:469008)
gene: Gria2, Glur2
expression_system_variant: ORIGAMI B (DE3)
expression_system_vector_type: PLASMID
expression_system_plasmid: PET-22B(+)
Authors : Frydenvang, K., Kastrup, J.S.
Keywords : IONOTROPIC GLUTAMATE RECEPTOR, GLUA2O LIGAND-BINDING DOMAIN, BICYCLIC PYRIMIDINEDIONE ANALOGUE, MEMBRANE PROTEIN
Exp. method : X-RAY DIFFRACTION ( 0.9990 Å )
Citation :

Ionotropic Glutamate Receptor GluA2 in Complex with Bicyclic Pyrimidinedione-Based Compounds: When Small Compound Modifications Have Distinct Effects on Binding Interactions.

Frydenvang, K.,Pickering, D.S.,Kshirsagar, G.U.  et al.
(2020)  Acs Chem Neurosci  11 : 1791 - 1800

PubMed: 32437601
DOI: 10.1021/acschemneuro.0c00195

Reaction

Chain : A
UniProt : P19491 (GRIA2_RAT)
Reaction: EC: Evidence:
Physiological Direction:
Ca(2+)(in) = Ca(2+)(out) - PubMed:11773314, PubMed:1653450
-
Na(+)(in) = Na(+)(out) - PubMed:11773314, PubMed:1653450
-