3C79 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF APLYSIA CALIFORNICA ACHBP IN COMPLEX WITH THE NEONICOTINOID IMIDACLOPRID

Authors :   T. T. Talley, M. Harel, R. E. Hibbs, M. Tomizawa, J. E. Casida, P. W. Taylo

Date :   06 Feb 08 (Deposition) - 20 May 08 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.48

Chains :   Asym./Biol. Unit : A,B,C,D,E

Keywords :   Protein-Neonicotinoid Complex, 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

Molecule 1 - SOLUBLE ACETYLCHOLINE RECEPTOR
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	KIDNEY HEK-293
	Expression System Common	:	HUMAN
	Organism Common	:	CALIFORNIA SEA HARE
	Organism Scientific	:	APLYSIA CALIFORNICA

		1	2	3	4	5
Asymmetric/Biological Unit	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 7)

No.	Name	Count	Type	Full Name
1	IM4	4	Ligand/Ion	(2E)-1-[(6-CHLOROPYRIDIN-3-YL)METHYL]-N-NITROIMIDAZOLIDIN-2-IMINE
2	IPA	3	Ligand/Ion	ISOPROPYL ALCOHOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TRP A:147 , TYR A:188 , SER A:189 , CYS A:190 , TYR A:195 , TYR E:55 , GLN E:57 , MET E:116 , ILE E:118	BINDING SITE FOR RESIDUE IM4 A 301
2	AC2	SOFTWARE	TYR A:55 , MET A:116 , ILE A:118 , TYR B:93 , TRP B:147 , TYR B:188 , SER B:189 , CYS B:190 , TYR B:195	BINDING SITE FOR RESIDUE IM4 B 302
3	AC3	SOFTWARE	TYR B:55 , MET B:116 , ILE B:118 , TRP C:147 , TYR C:188 , SER C:189 , CYS C:190 , TYR C:195	BINDING SITE FOR RESIDUE IM4 C 303
4	AC4	SOFTWARE	TYR C:55 , MET C:116 , ILE C:118 , TRP D:147 , TYR D:188 , CYS D:190 , TYR D:195	BINDING SITE FOR RESIDUE IM4 D 304
5	AC5	SOFTWARE	ARG B:183 , ARG C:183	BINDING SITE FOR RESIDUE IPA C 401
6	AC6	SOFTWARE	MET D:116 , ILE D:118 , TRP E:147	BINDING SITE FOR RESIDUE IPA D 402
7	AC7	SOFTWARE	THR A:91 , TYR A:93 , LYS A:143 , GLY A:145 , TRP A:147 , TYR A:188	BINDING SITE FOR RESIDUE IPA A 404

Asymmetric/Biological Unit

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

(no "Cis Peptide Bond" information available for 3C79)

(no "SAP(SNP)/Variant" information available for 3C79)

(no "PROSITE Motif" information available for 3C79)

(no "Exon" information available for 3C79)

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:211
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:211
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 
         Q8WSF8_APLCA    15 GQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 225
               SCOP domains d3c79a_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhhh...eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c79 A  -2 DKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     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:212
 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 d3c79b_ 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................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c79 B  -3 DDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain C from PDB  Type:PROTEIN  Length:208
 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 d3c79c_ C: automate  d matches                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.--.........eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhhh...eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3c79 C  -1 KLHSQANLMRLKSDLFNRS--YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     8        |- |      28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
                                             17 20

Chain D from PDB  Type:PROTEIN  Length:212
 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 d3c79d_ D: automated matches                                                                                                                                                                                         SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeee.hhhh.hhhhh....eeeee.hhh....eee.......ee....eeeee...eeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c79 D  -3 DDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain E from PDB  Type:PROTEIN  Length:211
 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 d3c79e_ E: 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................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3c79 E  -3 DDKLHSQANLMRLKSDLFNRS-MYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRERR 208
                                     6        16| |     26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206  
                                               17 |                                                                                                                                                                                             
                                                 19

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Nicotinic receptor ligand binding domain-like (58)

Superfamily: Nicotinic receptor ligand binding domain-like (58)

Family: automated matches (40)

Protein domain: automated matches (40)

California sea hare (Aplysia californica) [TaxId: 6500] (36)

1a	d3c79a_	A:
1b	d3c79b_	B:
1c	d3c79c_	C:
1d	d3c79d_	D:
1e	d3c79e_	E:

(no "CATH Domain" information available for 3C79)

(no "Pfam Domain" information available for 3C79)

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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3c79)

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	3c79
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 7)

Sites (7, 7)

SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (7, 7)

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