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(-) Description

Title :  STRUCTURE OF THE LIGAND-BINDING DOMAIN OF GLUK1 IN COMPLEX WITH THE ANTAGONIST CNG10111
 
Authors :  C. Moller, D. Tapken, J. S. Kastrup, K. Frydenvang
Date :  06 Mar 15  (Deposition) - 05 Aug 15  (Release) - 26 Aug 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.93
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ionotropic Glutamate Receptor, Kainate Receptor Gluk1, Ligand-Binding Domain, Antagonist, Signaling Protein, Fusion Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. Krogsgaard-Larsen, M. Storgaard, C. Mller, C. S. Demmer, J. Hansen L. Han, R. N. Monrad, B. Nielsen, D. Tapken, D. S. Pickering, J. S. Kastrup, K. Frydenvang, L. Bunch
Structure-Activity Relationship Study Of Ionotropic Glutamate Receptor Antagonist (2S, 3R)-3-(3-Carboxyphenyl)Pyrrolidine-2-Carboxylic Acid.
J. Med. Chem. V. 58 6131 2015
PubMed-ID: 26200741  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00750
(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
    Expression System Plasmid: PET28A
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GRIK1, GLUR5
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: THE PROTEIN COMPRISES SEGMENT S1 RESIDUES 445-559, A GT LINKER AND S2 RESIDUES 682-820
    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  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
14E72Ligand/Ion(3R,4S)-3-(3-CARBOXYPHENYL)-4-PROPYL-L-PROLINE
2ACT4Ligand/IonACETATE ION
3CL4Ligand/IonCHLORIDE ION
4EDO1Ligand/Ion1,2-ETHANEDIOL
5PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU A:13 , TYR A:61 , PRO A:88 , LEU A:89 , THR A:90 , ARG A:95 , THR A:142 , MET A:189 , GLU A:190 , SER A:193 , TYR A:216 , HOH A:457 , HOH A:461 , HOH A:474 , HOH A:482 , HOH A:560binding site for residue 4E7 A 301
02AC2SOFTWAREGLU A:175 , HOH A:414 , LEU B:12 , VAL B:56 , GLY B:59binding site for residue ACT A 302
03AC3SOFTWAREGLY A:62 , ALA A:63 , ARG A:95binding site for residue CL A 303
04AC4SOFTWARELYS A:103 , HOH A:497 , LYS B:103 , HOH B:459binding site for residue CL A 304
05AC5SOFTWARELEU A:55binding site for residue CL A 305
06AC6SOFTWAREHIS A:80 , PRO A:225 , HOH A:516binding site for residue PEG A 306
07AC7SOFTWAREGLU B:13 , TYR B:61 , PRO B:88 , LEU B:89 , THR B:90 , ARG B:95 , VAL B:137 , THR B:142 , MET B:189 , GLU B:190 , SER B:193 , TYR B:216 , HOH B:480 , HOH B:503 , HOH B:605 , HOH B:646binding site for residue 4E7 B 301
08AC8SOFTWARETHR A:10 , ILE A:11 , LEU A:12 , LEU A:55 , VAL A:56 , GLY A:59 , GLU B:175 , HOH B:426binding site for residue ACT B 302
09AC9SOFTWAREPRO B:119 , ILE B:120 , ASP B:125 , LYS B:128 , GLN B:129binding site for residue ACT B 303
10AD1SOFTWAREARG A:20 , SER A:22 , HOH B:442binding site for residue ACT B 304
11AD2SOFTWAREARG B:31 , LEU B:55binding site for residue CL B 305
12AD3SOFTWARELYS A:171 , ASN A:172 , HOH B:403 , HOH B:412binding site for residue EDO B 306

(-) 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 4YMB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YMB)

(-) 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:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh.eee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..eee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ymb A   4 RTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGCP 257
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253| 
                                                                                                                                                                                                                                                                                   253| 
                                                                                                                                                                                                                                                                                    256 


Chain B from PDB  Type:PROTEIN  Length:255
                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh.eeeeeeeeee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eeeeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ymb B   2 ANRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGC 256
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251
   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 4YMB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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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 5m2v 5mfq 5mfv 5mfw

(-) Related Entries Specified in the PDB File

4e0x 4E0X IS WITH SAME PROTEIN AND SIMILAR SCAFFOLD OF LIGAND