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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GLUK1 LIGAND-BINDING DOMAIN IN COMPLEX WITH KAINATE AND BPAM-521 AT 2.18 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 :  2.18
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 A 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, 10)

Asymmetric/Biological Unit (6, 10)
No.NameCountTypeFull Name
15PX2Ligand/Ion4-CYCLOPROPYL-3,4-DIHYDRO-7-HYDROXY-2H-1,2,4-BENZOTHIADIAZINE 1,1-DIOXIDE
2ACT1Ligand/IonACETATE ION
3CL1Ligand/IonCHLORIDE ION
4GOL1Ligand/IonGLYCEROL
5KAI2Ligand/Ion3-(CARBOXYMETHYL)-4-ISOPROPENYLPROLINE
6SO43Ligand/IonSULFATE ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:531 , PRO A:532 , PHE A:533 , MET A:534 , THR A:535 , LEU A:783 , GLN A:786 , LEU A:791 , HOH A:1001 , ILE B:519 , PRO B:532 , THR B:535 , LYS B:762 , GLY B:763binding site for residue 5PX A 901
02AC2SOFTWAREILE A:519 , PRO A:532 , THR A:535 , SER A:761 , LYS A:762 , GLY A:763 , LYS B:531 , PRO B:532 , PHE B:533 , MET B:534 , LEU B:783 , GLN B:786 , LEU B:791binding site for residue 5PX 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 , HOH A:1036 , HOH A:1048 , HOH A:1057binding site for residue KAI A 903
04AC4SOFTWARELYS A:531 , LYS B:531 , HOH B:1070binding site for residue CL A 904
05AC5SOFTWAREGLN A:786 , HIS A:792 , HOH A:1031 , ASP B:760 , SER B:761binding site for residue SO4 A 905
06AC6SOFTWARELYS A:488 , TYR A:489 , ARG A:686 , ASP A:687 , GLY A:688 , LYS A:719binding site for residue GOL A 906
07AC7SOFTWAREGLU 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:1023 , HOH B:1043 , HOH B:1072binding site for residue KAI B 901
08AC8SOFTWAREASP A:760 , SER A:761 , GLN B:786 , HIS B:792 , HOH B:1045 , HOH B:1079binding site for residue SO4 B 902
09AC9SOFTWAREARG B:459 , HOH B:1006binding site for residue SO4 B 903
10AD1SOFTWAREARG B:448 , SER B:450 , LYS B:452binding site for residue ACT B 904

(-) 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 5MFV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5MFV)

(-) 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:250
                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.......ee.......hhhh.eehhhhhhhhhhhhhhh..eeeee...............hhhhhhhhh....ee......hhhhhh.eeeeeeeeeeeeeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhhhh..eeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mfv A 432 RTLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNDKGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRG 801
                                   441       451       461       471       481       491       501       511       521       531       541    || 671       681       691       701       711       721       731       741       751       761       771       781       791       801
                                                                                                                                            546|                                                                                                                                      
                                                                                                                                             667                                                                                                                                      


Chain B 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.eeeeeeeeeeeeeeeee......hhhhhhh....eee....hhhhhhhhhh.hhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.eeeeeehhhhhhhhh....eeeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mfv B 433 TLIVTTILEEPYVMYRKSDKPLYGNDRFEGYCLDLLKELSNILGFLYDVKLVPDGKYGAQNGEWNGMVKELIDHRADLAVAPLTITYVREKVIDFSKPFMTLGISILYRKGTPIDSADDLAKQTKIEYGAVRDGSTMTFFKKSKISTYEKMWAFMSSRQQSALVKNSDEGIQRVLTTDYALLMESTSIEYVTQRNCNLTQIGGLIDSKGYGVGTPIGSPYRDKITIAILQLQEEGKLHMMKEKWWRGNGCP 805
                                   442       452       462       472       482       492||     504       514       524       534       544 ||    674       684       694       704       714       724       734       744       754       764       774       784       794       804 
                                                                                      493|                                               546|                                                                                                                                          
                                                                                       496                                                667
   Legend:   → Mismatch (orange background)
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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 5MFV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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 5mfw

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