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(-) Description

Title :  CRYSTAL STRUCTURE OF A COMPLEX OF ACHBP FROM APLYSIA CALIFORNICA AND THE NEONICOTINOID THIACLOPRID
 
Authors :  T. T. Talley, M. Harel, R. E. Hibbs, M. Tomizawa, J. E. Casida, P. W. Taylo
Date :  08 Feb 08  (Deposition) - 20 May 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Acetylcholine Binding Protein, Neonicotinoid, Receptor, Choline- Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  T. T. Talley, M. Harel, R. E. Hibbs, Z. Radic, M. Tomizawa, J. E. Casida, P. Taylor
Atomic Interactions Of Neonicotinoid Agonists With Achbp: Molecular Recognition Of The Distinctive Electronegative Pharmacophore.
Proc. Natl. Acad. Sci. Usa V. 105 7606 2008
PubMed-ID: 18477694  |  Reference-DOI: 10.1073/PNAS.0802197105

(-) Compounds

Molecule 1 - SOLUBLE ACETYLCHOLINE RECEPTOR
    ChainsA, B, C, D, E
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineKIDNEY HEK-293
    Expression System CommonHUMAN
    Organism CommonCALIFORNIA SEA HARE
    Organism ScientificAPLYSIA CALIFORNICA

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1IPA7Ligand/IonISOPROPYL ALCOHOL
2MG2Ligand/IonMAGNESIUM ION
3TH44Ligand/Ion{(2Z)-3-[(6-CHLOROPYRIDIN-3-YL)METHYL]-1,3-THIAZOLIDIN-2-YLIDENE}CYANAMIDE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETRP A:147 , TYR A:188 , SER A:189 , CYS A:190 , TYR A:195 , TYR E:55 , MET E:116 , ILE E:118BINDING SITE FOR RESIDUE TH4 A 301
02AC2SOFTWARETYR A:55 , MET A:116 , ILE A:118 , TRP B:147 , TYR B:188 , CYS B:190 , TYR B:195BINDING SITE FOR RESIDUE TH4 B 302
03AC3SOFTWARETYR B:55 , MET B:116 , ILE B:118 , TRP C:147 , TYR C:188 , SER C:189 , CYS C:190 , TYR C:195BINDING SITE FOR RESIDUE TH4 C 303
04AC4SOFTWARETYR C:55 , MET C:116 , ILE C:118 , TYR D:93 , TRP D:147 , TYR D:188 , CYS D:190 , TYR D:195BINDING SITE FOR RESIDUE TH4 D 304
05AC5SOFTWARETHR D:91 , ALA D:92 , TYR D:93 , GLY D:145 , SER D:146 , TRP D:147 , TYR D:188BINDING SITE FOR RESIDUE IPA D 401
06AC6SOFTWAREARG B:183 , ARG C:183BINDING SITE FOR RESIDUE IPA C 402
07AC7SOFTWARETYR A:93 , LYS A:143 , PHE A:144 , GLY A:145 , TYR A:188BINDING SITE FOR RESIDUE IPA A 404
08AC8SOFTWAREMET D:116 , ILE D:118BINDING SITE FOR RESIDUE IPA D 405
09AC9SOFTWAREGLY C:145 , SER C:146 , TYR C:188BINDING SITE FOR RESIDUE IPA C 406
10BC1SOFTWARETHR B:91 , TYR B:93 , GLY B:145 , SER B:146 , TRP B:147 , TYR B:188BINDING SITE FOR RESIDUE IPA B 407
11BC2SOFTWAREGLN C:38 , SER C:167 , TYR C:169BINDING SITE FOR RESIDUE IPA C 408

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:127 -A:140
2A:190 -A:191
3B:127 -B:140
4B:190 -B:191
5C:127 -C:140
6C:190 -C:191
7D:127 -D:140
8D:190 -D:191
9E:127 -E:140
10E:190 -E:191

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3C84)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3C84)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3C84)

(-) Exons   (0, 0)

(no "Exon" information available for 3C84)

(-) 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:210
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:210
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
         Q8WSF8_APLCA    15 GQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d3c84a_ A: automated matches                                                                                                                                                                                       SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c84 A  -2 DKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     7        17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207

Chain B from PDB  Type:PROTEIN  Length:210
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:212
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223  
         Q8WSF8_APLCA    14 VGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 225
               SCOP domains d3c84b_ B: automated   matches                                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh..--.........eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c84 B  -3 DDKLHSQANLMRLKSDLFNRS--YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     6        16|  |    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206  
                                               17 20                                                                                                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:208
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:210
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
         Q8WSF8_APLCA    15 GQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d3c84c_ C: automated   matches                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh..--.........eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c84 C  -2 DKLHSQANLMRLKSDLFNRS--YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     7        17  |     27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                              17 20                                                                                                                                                                                           

Chain D from PDB  Type:PROTEIN  Length:209
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:210
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225
         Q8WSF8_APLCA    16 QAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 225
               SCOP domains d3c84d_ D: automated  matches                                                                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh...-.........eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhh....eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c84 D  -1 KLHSQANLMRLKSDLFNRSP-YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     8        18 |      28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
                                              18 |                                                                                                                                                                                            
                                                20                                                                                                                                                                                            

Chain E from PDB  Type:PROTEIN  Length:205
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:210
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
         Q8WSF8_APLCA    15 GQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d3c84e_ E: automa     ted matches                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhh-----.........eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee.hhhhhh...eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c84 E  -2 DKLHSQANLMRLKSDLF-----YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     7      |  -  |     27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                           14    20                                                                                                                                                                                           

   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  (1, 5)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3C84)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3C84)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q8WSF8_APLCA | Q8WSF8)
molecular function
    GO:0005230    extracellular ligand-gated ion channel activity    Enables the transmembrane transfer of an ion by a channel that opens when a specific extracellular ligand has been bound by the channel complex or one of its constituent parts.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0034220    ion transmembrane transport    A process in which an ion is transported from one side of a membrane to the other by means of some agent such as a transporter or pore.
    GO:0006811    ion transport    The directed movement of charged atoms or small charged molecules into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/TrEMBL
        Q8WSF8_APLCA | Q8WSF82br7 2br8 2byn 2byp 2byq 2byr 2bys 2c9t 2pgz 2ph9 2uz6 2w8f 2w8g 2wn9 2wnc 2wnj 2wnl 2wzy 2x00 2xnt 2xnu 2xnv 2xys 2xyt 2xz5 2xz6 2y54 2y56 2y57 2y58 2y7y 2ymd 2yme 3c79 3gua 3peo 3pmz 3sh1 3sio 3t4m 4aft 4bfq 4bqt 4dbm 4ez1 4frr 4wv9 4xhe 4xk9 4zjs 4zk4 5ain 5brx 5bw2 5co5 5jme 5ke4 5kzu 5lxb 5syo 5tvc

(-) Related Entries Specified in the PDB File

3c79