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(-) Description

Title :  STRUCTURE OF GLUK1 LIGAND-BINDING DOMAIN (S1S2) IN COMPLEX WITH (S)-2-AMINO-4-(2,3-DIOXO-1,2,3,4-TETRAHYDROQUINOXALIN-6-YL)BUTANOIC ACID AT 2.28 A RESOLUTION
 
Authors :  C. M. Kristensen, K. Frydenvang, J. S. Kastrup
Date :  20 May 14  (Deposition) - 22 Apr 15  (Release) - 01 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.28
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B  (2x)
Keywords :  Kainate Receptor Ligand-Binding Domain, Gluk1-S1S2, Antagonist, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. S. Demmer, C. Mller, P. M. Brown, L. Han, D. S. Pickering, B. Nielsen, D. Bowie, K. Frydenvang, J. S. Kastrup, L. Bunch
Binding Mode Of An Alpha-Amino Acid-Linked Quinoxaline-2, 3-Dione Analogue At Glutamate Receptor Subtyp Gluk1.
Acs Chem Neurosci V. 6 845 2015
PubMed-ID: 25856736  |  Reference-DOI: 10.1021/ACSCHEMNEURO.5B00038

(-) Compounds

Molecule 1 - GLUTAMATE RECEPTOR IONOTROPIC, KAINATE 1
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A(+)
    Expression System Strain: ORIGAMI 2
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 445-559, 682-820
    Gene: GLUR5, GRIK1
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Strain: RAT
    Synonym: GLUK1, GLUTAMATE RECEPTOR 5, GLUR-5, GLUR5

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A C
Biological Unit 2 (2x):  B 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 14)

Asymmetric Unit (6, 14)
No.NameCountTypeFull Name
135K3Ligand/Ion(2S)-2-AMINO-4-(2,3-DIOXO-1,2,3,4-TETRAHYDROQUINOXALIN-6-YL)BUTANOIC ACID
2ACT1Ligand/IonACETATE ION
3CL1Ligand/IonCHLORIDE ION
4GOL3Ligand/IonGLYCEROL
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6SO44Ligand/IonSULFATE ION
Biological Unit 1 (4, 6)
No.NameCountTypeFull Name
135K2Ligand/Ion(2S)-2-AMINO-4-(2,3-DIOXO-1,2,3,4-TETRAHYDROQUINOXALIN-6-YL)BUTANOIC ACID
2ACT1Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4GOL-1Ligand/IonGLYCEROL
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6SO42Ligand/IonSULFATE ION
Biological Unit 2 (4, 14)
No.NameCountTypeFull Name
135K2Ligand/Ion(2S)-2-AMINO-4-(2,3-DIOXO-1,2,3,4-TETRAHYDROQUINOXALIN-6-YL)BUTANOIC ACID
2ACT-1Ligand/IonACETATE ION
3CL-1Ligand/IonCHLORIDE ION
4GOL6Ligand/IonGLYCEROL
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6SO44Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:16 , TYR A:61 , PRO A:88 , LEU A:89 , THR A:90 , ARG A:95 , THR A:192 , SER A:193 , TYR A:216 , HOH A:417BINDING SITE FOR RESIDUE 35K A 301
02AC2SOFTWAREGLY A:140 , SER A:141 , THR A:142 , GLU A:190 , HOH A:429 , HOH A:453BINDING SITE FOR RESIDUE SO4 A 302
03AC3SOFTWAREARG A:31 , LYS A:54 , LEU A:55 , GLU A:133 , SER A:167 , ARG A:179BINDING SITE FOR RESIDUE PG4 A 303
04AC4SOFTWARELYS A:171 , ASN A:172BINDING SITE FOR RESIDUE CL A 304
05AC5SOFTWAREGLU B:13 , TYR B:16 , TYR B:61 , PRO B:88 , LEU B:89 , THR B:90 , ARG B:95 , THR B:192 , SER B:193 , TYR B:216 , HOH B:425 , HOH B:448 , HOH B:449 , HOH B:472BINDING SITE FOR RESIDUE 35K B 301
06AC6SOFTWARESER B:141 , THR B:142 , GLU B:190 , HOH B:413 , HOH B:462 , HOH B:463 , HOH B:482BINDING SITE FOR RESIDUE SO4 B 302
07AC7SOFTWAREILE A:151 , SER A:152 , LYS B:229 , HOH B:429BINDING SITE FOR RESIDUE SO4 B 303
08AC8SOFTWAREASP B:212 , HIS B:244 , HOH B:456BINDING SITE FOR RESIDUE GOL B 304
09AC9SOFTWAREARG B:31 , LEU B:55BINDING SITE FOR RESIDUE GOL B 305
10BC1SOFTWAREARG B:179 , HOH B:438 , ARG C:31 , HOH C:441BINDING SITE FOR RESIDUE GOL B 306
11BC2SOFTWAREGLU B:96 , PHE B:101 , SER B:102 , LYS B:103 , ARG B:227 , ASP B:228 , THR B:231BINDING SITE FOR RESIDUE PG4 B 307
12BC3SOFTWAREGLU C:13 , GLU C:14 , TYR C:16 , TYR C:61 , PRO C:88 , THR C:90 , ARG C:95 , THR C:192 , TYR C:216BINDING SITE FOR RESIDUE 35K C 301
13BC4SOFTWAREVAL C:137 , GLY C:140 , SER C:141 , THR C:142 , MET C:189 , GLU C:190BINDING SITE FOR RESIDUE SO4 C 302
14BC5SOFTWARESER A:213 , HIS C:244 , HOH C:432BINDING SITE FOR RESIDUE ACT C 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QF9)

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:14 -Pro A:15
2Glu B:14 -Pro B:15
3Glu C:14 -Pro C:15

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QF9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QF9)

(-) Exons   (0, 0)

(no "Exon" information available for 4QF9)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....eeeeeee...hhhh.eee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qf9 A   5 TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGN 254
                                    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


Chain B from PDB  Type:PROTEIN  Length:252
                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh.eeeeee...............hhhhhhhhh....ee......hhhhhh..ee....eee.eeeeee......hhhhhhh....eeee...hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..ee.....hhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qf9 B   3 NRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGN 254
                                    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  


Chain C from PDB  Type:PROTEIN  Length:244
                                                                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......ee.......hhhh.eehhhhhhhhhhhh.....eeeee...............hhhhhhhhh....ee......hhhhhh.eee....eeeeeeeeee......hhhhhhh....eee....hhhhhhhhh..hhhhhhhhhhhh......hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeeeeeeeeeeee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qf9 C   5 TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWW 251
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       167       177       187       197       207       217       227       237       247    
                                                                                                                                                                                        163|                                                                                    
                                                                                                                                                                                         167
   Legend:   → Mismatch (orange background)
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    → 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 4QF9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QF9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QF9)

(-) Gene Ontology  (33, 33)

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        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 4ymb 5m2v 5mfq 5mfv 5mfw

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