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(-) Description

Title :  CRYSTAL STRUCTURE OF THE KAINATE RECEPTOR GLUK3 LIGAND BINDING DOMAIN IN COMPLEX WITH (S)-GLUTAMATE
 
Authors :  R. Venskutonyte, K. Frydenvang, M. Gajhede, J. S. Kastrup
Date :  29 Aug 13  (Deposition) - 16 Oct 13  (Release) - 16 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Agonist, Membrane, Receptor, Receptor-Agonist Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Venskutonyte, K. Frydenvang, M. Gajhede, L. Bunch, D. S. Pickering J. S. Kastrup
Binding Site And Interlobe Interactions Of The Ionotropic Glutamate Receptor Gluk3 Ligand Binding Domain Revealed By High Resolution Crystal Structure In Complex With (S)-Glutamate.
J. Struct. Biol. V. 176 307 2011
PubMed-ID: 21907808  |  Reference-DOI: 10.1016/J.JSB.2011.08.014

(-) 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: GRIK3, GLUR7
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: GLUK3, GLUTAMATE RECEPTOR 7, GLUR-7, GLUR7

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 6)

Asymmetric Unit (4, 6)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2GGL1Ligand/IonGAMMA-L-GLUTAMIC ACID
3GOL1Ligand/IonGLYCEROL
4K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2GGL2Ligand/IonGAMMA-L-GLUTAMIC ACID
3GOL2Ligand/IonGLYCEROL
4K-1Ligand/IonPOTASSIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:63 , PRO A:90 , LEU A:91 , THR A:92 , ARG A:97 , GLY A:142 , ALA A:143 , THR A:144 , GLU A:191 , HOH A:408 , HOH A:411 , HOH A:412 , HOH A:440BINDING SITE FOR RESIDUE GGL A 301
2AC2SOFTWAREASN A:5 , SER A:52 , HOH A:401 , HOH A:482BINDING SITE FOR RESIDUE K A 302
3AC3SOFTWARESER A:24 , ARG A:26 , HOH A:448 , HOH A:555 , HOH A:669 , HOH A:670BINDING SITE FOR RESIDUE K A 303
4AC4SOFTWAREARG A:33 , LEU A:57BINDING SITE FOR RESIDUE CL A 304
5AC5SOFTWAREGLN A:239 , ASP A:242 , LEU A:244 , HIS A:245BINDING SITE FOR RESIDUE CL A 305
6AC6SOFTWARELYS A:99 , THR A:109 , HOH A:436 , HOH A:558 , HOH A:581 , HOH A:608BINDING SITE FOR RESIDUE GOL A 306

(-) SS Bonds  (1, 1)

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

(-) Cis Peptide Bonds  (1, 1)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MH5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MH5)

(-) Exons   (0, 0)

(no "Exon" information available for 4MH5)

(-) Sequences/Alignments

Asymmetric 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 d4mh5a_ A: automated matches                                                                                                                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....eeeeeee.hhhhhh.eee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhh.hhhhh..hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mh5 A   3 GTNRSLIVTTLLEEPFVMFRKSDRTLYGNDRFEGYCIDLLKELAHILGFSYEIRLVEDGKYGAQDDKGQWNGMVKELIDHKADLAVAPLTITHVREKAIDFSKPFMTLGVSILYRKGTPIDSADDLAKQTKIEYGAVKDGATMTFFKKSKISTFEKMWAFMSSKPSALVKNNEEGIQRTLTADYALLMESTTIEYITQRNCNLTQIGGLIDSKGYGIGTPMGSPYRDKITIAILQLQEEDKLHIMKEKWWRGSGCP 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
   Legend:   → Mismatch (orange background)
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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  (1, 1)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MH5)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MH5)

(-) Gene Ontology  (24, 24)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

(-) Related Entries Specified in the PDB File

3s9e THIS ENTRY (3S9E) WAS SOLVED USING THE SAME DATA BUT IN A LOWER SYMMETRY SPACE GROUP (P41). THE CURRENT ENTRY IS THEREFORE THE SAME EXPERIMENT, BUT WITH THE DATA REPROCESSED AND THE STRUCTURE SOLVED IN SPACE GROUP P4122.