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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KAINATE RECEPTOR GLUK3 LIGAND-BINDING DOMAIN IN COMPLEX WITH THE AGONIST (2S,4R)-4-(3-METHYLAMINO-3-OXOPROPYL) GLUTAMIC ACID AT 2.6 A RESOLUTION
 
Authors :  R. Venskutonyte, A. P. Larsen, K. Frydenvang, M. Gajhede, J. S. Kastrup
Date :  06 Dec 13  (Deposition) - 06 Aug 14  (Release) - 22 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Kainate Receptor, Ligand Binding Domain, Agonist, Ionotropic Glutamate Receptor, Membrabe Protein-Agonist Complex, Membrane Protein-Agonist Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Venskutonyte, A. P. Larsen, K. Frydenvang, M. Gajhede, E. Sagot, Z. Assaf, T. Gefflaut, D. S. Pickering, L. Bunch, J. S. Kastrup
Molecular Recognition Of Two 2, 4-Syn-Functionalized (S)-Glutamate Analogues By The Kainate Receptor Gluk3 Ligan Binding Domain.
Chemmedchem V. 9 2254 2014
PubMed-ID: 25044437  |  Reference-DOI: 10.1002/CMDC.201402204
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: POPINJ
    Expression System Strain: ORIGAMI 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 432-546 AND UNP RESIDUES 669-806
    Gene: GLUR7, GRIK3
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUK3, GLUTAMATE RECEPTOR 7, GLUR-7, GLUR7

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
12QD1Ligand/Ion(4R)-4-[3-(METHYLAMINO)-3-OXOPROPYL]-L-GLUTAMIC ACID
2CL1Ligand/IonCHLORIDE ION
3K2Ligand/IonPOTASSIUM ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:15 , TYR A:63 , PRO A:90 , LEU A:91 , THR A:92 , ARG A:97 , GLY A:142 , ALA A:143 , THR A:144 , ASN A:174 , GLU A:191 , THR A:194 , TYR A:217BINDING SITE FOR RESIDUE 2QD A 301
2AC2SOFTWARESER A:24 , ARG A:26BINDING SITE FOR RESIDUE K A 302
3AC3SOFTWAREASN A:5 , SER A:52 , HOH A:405BINDING SITE FOR RESIDUE K A 303
4AC4SOFTWAREARG A:33 , ARG A:56 , LEU A:57BINDING SITE FOR RESIDUE CL A 304

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:203 -A:257

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:16 -Pro A:17

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NWD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NWD)

(-) Exons   (0, 0)

(no "Exon" information available for 4NWD)

(-) 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:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee..............ee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhh........hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nwd A   5 NRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRKGTPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGSGCP 258
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254
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  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 4NWD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NWD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NWD)

(-) Gene Ontology  (24, 24)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        GRIK3_RAT | P42264: 3olz 3s9e 3u92 3u93 3u94 4e0w 4g8n 4igr 4mh5 4nwc

(-) Related Entries Specified in the PDB File

3s9e 4mh5 4nwc