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(-) Description

Title :  STRUCTURE OF GLUK1 LIGAND-BINDING DOMAIN (S1S2) IN COMPLEX WITH (2S, 4R)-4-(2-CARBOXYPHENOXY)PYRROLIDINE-2-CARBOXYLIC ACID AT 3.18 A RESOLUTION
 
Authors :  K. Frydenvang, J. S. Kastrup, C. M. Kristensen
Date :  13 Oct 16  (Deposition) - 11 Jan 17  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Kainate Receptor Ligand-Binding Domain, Gluk1-Lbd, Gluk1-S1S2, Antagonist, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Krogsgaard-Larsen, C. G. Delgar, K. Koch, P. M. Brown, C. Mller, L. Han, T. H. Huynh, S. W. Hansen, B. Nielsen, D. Bowie, D. S. Pickering, J. S. Kastrup, K. Frydenvang, L. Bunch
Design And Synthesis Of A Series Of L-Trans-4-Substituted Prolines As Selective Antagonists For The Ionotropic Glutamate Receptors Including Functional And X-Ray Crystallographic Studies Of New Subtype Selective Kainic Acid Receptor Subtype 1 (Gluk1) Antagonist (2S, 4R)-4-(2-Carboxyphenoxy)Pyrrolidine-2-Carboxylic Acid.
J. Med. Chem. V. 60 441 2017
PubMed-ID: 28005385  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.6B01516
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 1,GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 1
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: ORIGAMI 2
    Expression System Vector: PET28A(+)
    Expression System Vector Type: PLASMID
    Gene: GRIK1, GLUR5
    Organism Common: NORWAY RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: NATIVE GLUK1 IS A MEMBRANE PROTEIN. THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND-BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUE 117-118). THE SEQUENCE MATCHES DISCONTINOUSLY WITH REFERENCE DATABASE (430-544, 667-805). GLY1 IS A CLONING REMNANCE. ISOFORM GLUR5-2. THE CONFLICT OF GLY34 IS REFERED TO ALA - GLY SEQUENCE CONFLICT AT RESIDUE 462 IN UNP DATABASE
    Synonym: GLUK1,GLUTAMATE RECEPTOR 5,GLUR5,GLUK1,GLUTAMATE RECEPTOR 5, GLUR5

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
17E52Ligand/Ion(2~{S},4~{R})-4-(2-CARBOXYPHENOXY)PYRROLIDINE-2-CARBOXYLIC ACID
2CL2Ligand/IonCHLORIDE ION
3SO46Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:61 , PRO A:88 , LEU A:89 , THR A:90 , ARG A:95 , SER A:141 , THR A:142 , SER A:173 , MET A:189 , GLU A:190 , SER A:193binding site for residue 7E5 A 301
02AC2SOFTWAREHIS A:244 , LYS A:247binding site for residue SO4 A 302
03AC3SOFTWAREARG A:31binding site for residue SO4 A 303
04AC4SOFTWARESER A:22binding site for residue SO4 A 304
05AC5SOFTWAREGLN A:238 , SER B:213binding site for residue CL A 305
06AC6SOFTWAREGLU B:13 , TYR B:61 , PRO B:88 , LEU B:89 , THR B:90 , ARG B:95 , SER B:141 , THR B:142 , MET B:189 , GLU B:190 , SER B:193binding site for residue 7E5 B 301
07AC7SOFTWAREHIS B:244 , LYS B:247binding site for residue SO4 B 302
08AC8SOFTWAREGLU A:133 , ARG B:31binding site for residue SO4 B 303
09AC9SOFTWAREARG B:227binding site for residue SO4 B 304
10AD1SOFTWAREGLN B:238binding site for residue CL B 305

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:202 -A:256
2B:202 -B:256

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:14 -Pro A:15
2Glu B:14 -Pro B:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5M2V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5M2V)

(-) Exons   (0, 0)

(no "Exon" information available for 5M2V)

(-) 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:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh..ee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m2v A   5 TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGCP 257
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       256 
                                                                                                                                                                                                                                                                                 252|  
                                                                                                                                                                                                                                                                                  255  


Chain B from PDB  Type:PROTEIN  Length:253
                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh..ee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeee......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5m2v B   5 TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 257
                                    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
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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 5M2V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5M2V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5M2V)

(-) Gene Ontology  (33, 33)

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
        GRIK1_RAT | P22756: 1txf 1vso 1ycj 2f34 2f35 2f36 2ojt 2pbw 2qs1 2qs2 2qs3 2qs4 2wky 3c31 3c32 3c33 3c34 3c35 3c36 3gba 3gbb 3s2v 4dld 4e0x 4qf9 4ymb 5mfq 5mfv 5mfw

(-) Related Entries Specified in the PDB File

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