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(-) Description

Title :  STRUCTURE OF THE LIGAND-BINDING DOMAIN OF THE IONOTROPIC GLUTAMATE RECEPTOR-LIKE GLUD2 IN COMPLEX WITH 7-CKA
 
Authors :  P. Naur, M. Gajhede, J. S. Kastrup
Date :  01 Jul 15  (Deposition) - 30 Dec 15  (Release) - 20 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Ionotropic Glutamate Receptor, Glud2, Ligand Binding Domain, Nmda Receptor Antagonist, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. S. Kristensen, K. B. Hansen, P. Naur, L. Olsen, N. L. Kurtkaya, S. M. Dravid, T. Kvist, F. Yi, J. Phlsgaard, R. P. Clausen, M. Gajhede, J. S. Kastrup, S. F. Traynelis
Pharmacology And Structural Analysis Of Ligand Binding To The Orthosteric Site Of Glutamate-Like Glud2 Receptors.
Mol. Pharmacol. V. 89 253 2016
PubMed-ID: 26661043  |  Reference-DOI: 10.1124/MOL.115.100909
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, DELTA-2
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PET28
    Expression System Taxid: 83333
    Expression System Variant: ORIGAMI 2
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 441-551,UNP RESIDUES 664-813
    Gene: GRID2
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUR DELTA-2 SUBUNIT

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1CKA3Ligand/Ion7-CHLOROKYNURENIC ACID
2CL1Ligand/IonCHLORIDE ION
3GOL1Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:12 , PHE A:15 , TYR A:58 , ALA A:85 , LEU A:86 , THR A:87 , ARG A:92 , ALA A:138 , TRP A:193 , ASP A:194 , VAL A:197 , TYR A:222 , HOH A:403binding site for residue CKA A 301
2AC2SOFTWAREVAL A:107 , HIS A:142 , VAL A:143 , TYR A:157 , MET A:160 , ASN A:215 , VAL A:217binding site for residue CKA A 302
3AC3SOFTWAREVAL A:174 , ALA A:179 , GLN A:182 , LYS A:183binding site for residue CKA A 303
4AC4SOFTWARELEU A:11 , GLU A:12 , HIS A:56 , TYR A:58 , HOH A:401 , HOH A:405binding site for residue GOL A 304
5AC5SOFTWARETYR A:48binding site for residue CL A 305

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CC2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:13 -Pro A:14

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CC2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CC2)

(-) Exons   (0, 0)

(no "Exon" information available for 5CC2)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:256
                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.......eeeeee..eeeeeehhhhhhhhhhhhhhh.eeeeee...............hhhhhhhhh....eeeeeee...hhhh.eeeeeeeeeeeeeeeee......hhhhhhh.....ee....hhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh..eeeeehhhhhhhhhhh....eeeeeeeeeeeeeeeeee....hhhhhhhhhhhhhhh.hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cc2 A   3 VVLRVVTVLEEPFVMVSENVLGKPKKYQGFSIDVLDALSNYLGFNYEIYVAPDHKYGSPQEDGTWNGLVGELVFKRADIGISALTITPDRENVVDFTTRYMDYSVGVLLRRGTSIQSLQDLSKQTDIPYGTVLDSAVYQHVRMKGLNPFERDSMYSQMWRMINRSNGSENNVLESQAGIQKVKYGNYAFVWDAAVLEYVAINDPDCSFYTVGNTVADRGYGIALQHGSPYRDVFSQRILELQQSGDMDILKHKWWP 258
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252
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  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5CC2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CC2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CC2)

(-) Gene Ontology  (21, 21)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Glu A:13 - Pro A:14   [ RasMol ]  
 

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        GRID2_RAT | Q63226: 2v3t 2v3u 5l2e

(-) Related Entries Specified in the PDB File

2v3t 2V3T CONTAINS THE SAME PROTEIN IN ITS APO FORM
2v3u 2V3U CONTAINS THE SAME PROTEIN IN COMPLEX WITH D-SERINE