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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUK1 LIGAND-BINDING DOMAIN IN COMPLEX WITH KAINATE AND BPAM-121 AT 2.10 A RESOLUTION
 
Authors :  A. P. Larsen, K. Frydenvang, J. S. Kastrup
Date :  18 Nov 16  (Deposition) - 12 Apr 17  (Release) - 10 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ionotropic Glutamate Receptor, Gluk1 Ligand-Binding Domain, Membrane Protein, Positive Allosteric Modulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. P. Larsen, S. Fievre, K. Frydenvang, P. Francotte, B. Pirotte, J. S. Kastrup, C. Mulle
Identification And Structure-Function Study Of Positive Allosteric Modulators Of Kainate Receptors.
Mol. Pharmacol. V. 91 576 2017
PubMed-ID: 28360094  |  Reference-DOI: 10.1124/MOL.116.107599
(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 Variant: ORIGAMI 2
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 445-559,UNP RESIDUES 682-820
    Gene: GRIK1, GLUR5
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: THE PROTEIN CRYSTALLIZED IS THE EXTRACELLULAR LIGAND BINDING DOMAIN OF GLUK1. TRANSMEMBRANE REGIONS WERE GENETICALLY REMOVED AND REPLACED WITH A GLY-THR LINKER (RESIDUES 545 AND 546 OF THE STRUCTURE). THEREFORE, THE SEQUENCE MATCHES DISCONTINUOUSLY WITH THE REFERENCE DATABASE (430-544, 667-805). RESIDUE 429 IS REMNANT FROM CLONING.
    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  (6, 13)

Asymmetric/Biological Unit (6, 13)
No.NameCountTypeFull Name
17M62Ligand/Ion7-CHLORO-4-(2-FLUOROETHYL)-2,3-DIHYDRO-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE
2ACT1Ligand/IonACETATE ION
3CL1Ligand/IonCHLORIDE ION
4GOL2Ligand/IonGLYCEROL
5KAI2Ligand/Ion3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
6SO45Ligand/IonSULFATE ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:531 , PRO A:532 , PHE A:533 , MET A:534 , THR A:535 , LEU A:783 , GLN A:786 , HOH A:1072 , HOH A:1122 , ILE B:519 , PRO B:532 , THR B:535 , SER B:761 , LYS B:762 , GLY B:763 , 7M6 B:901 , HOH B:1120 , HOH B:1136binding site for residue 7M6 A 901
02AC2SOFTWARELYS A:531 , HOH A:1084 , LYS B:531 , HOH B:1076binding site for residue CL A 902
03AC3SOFTWAREGLU A:441 , TYR A:489 , PRO A:516 , THR A:518 , ARG A:523 , GLY A:688 , SER A:689 , THR A:690 , SER A:721 , GLU A:738 , GOL A:907 , HOH A:1013 , HOH A:1066 , HOH A:1110binding site for residue KAI A 903
04AC4SOFTWAREARG A:448 , SER A:450 , LYS B:695 , TRP B:706binding site for residue SO4 A 904
05AC5SOFTWAREARG A:459 , HOH A:1029 , HOH A:1065 , HOH A:1137 , HOH B:1002binding site for residue SO4 A 905
06AC6SOFTWAREASP A:451 , HOH A:1016 , SER B:711 , ARG B:712 , ASN B:751binding site for residue SO4 A 906
07AC7SOFTWARELYS A:488 , TYR A:489 , GLY A:490 , ALA A:491 , ASN A:499 , VAL A:685 , ARG A:686 , ASP A:687 , KAI A:903 , HOH A:1068 , HOH A:1117 , HOH A:1132binding site for residue GOL A 907
08AC8SOFTWARELYS A:488 , LYS A:719 , HOH A:1083 , LYS B:488 , LYS B:719binding site for residue ACT A 908
09AC9SOFTWAREPRO A:532 , MET A:534 , THR A:535 , SER A:761 , LYS A:762 , GLY A:763 , 7M6 A:901 , HOH A:1090 , LYS B:531 , PRO B:532 , PHE B:533 , MET B:534 , THR B:535 , LEU B:783 , GLN B:786 , HOH B:1131binding site for residue 7M6 B 901
10AD1SOFTWAREGLU B:441 , TYR B:489 , PRO B:516 , THR B:518 , ARG B:523 , GLY B:688 , SER B:689 , THR B:690 , GLU B:738 , HOH B:1021 , HOH B:1039binding site for residue KAI B 902
11AD2SOFTWAREHOH A:1002 , ARG B:459 , LYS B:482 , LEU B:483 , HOH B:1003 , HOH B:1008 , HOH B:1028 , HOH B:1122binding site for residue SO4 B 903
12AD3SOFTWAREGLN A:713 , ARG B:448 , SER B:450 , LYS B:452 , HOH B:1081binding site for residue SO4 B 904
13AD4SOFTWARELYS B:488 , TYR B:489 , GLY B:490 , ALA B:491 , ASN B:499 , ARG B:686 , ASP B:687 , GLY B:688 , HOH B:1050binding site for residue GOL B 905

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1B:750 -B:804

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Glu A:442 -Pro A:443
2Glu B:442 -Pro B:443

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MFW)

(-) 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:249
                                                                                                                                                                                                                                                                                         
               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
                 5mfw A 431 NRTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWW 799
                                   440       450       460       470       480       490       500       510       520       530       540     ||670       680       690       700       710       720       730       740       750       760       770       780       790         
                                                                                                                                             546|                                                                                                                                    
                                                                                                                                              667                                                                                                                                    


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.eee....eee.eeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeee......eee..eee....hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mfw B 433 TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 805
                                   442       452       462       472       482       492       502       512       522       532       542   ||  672       682       692       702       712       722       732       742       752       762       772       782       792       802   
                                                                                                                                           546|                                                                                                                                          
                                                                                                                                            667
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 5MFW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (33, 33)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
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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 4qf9 4ymb 5m2v 5mfq 5mfv

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