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Asym./Biol. Unit (Jmol Viewer)

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Title :   APLYSIA CALIFORNICA-ACHBP IN COMPLEX WITH TRIAZOLE 18

Authors :   A. Nemecz, J. G. Yamauchi, C. Kim

Date :   16 Jan 12 (Deposition) - 21 Mar 12 (Release) - 13 Jun 12 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   In Situ Click-Chemistry, Achbp, Nicotinic, Triazole, Tropane, Quinolinone, Cys-Loop Receptor Homologue, Acetylcholine-Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. P. Grimster, B. Stump, J. R. Fotsing, T. Weide, T. T. Talley, J. G. Yamauchi, Nemecz, C. Kim, K. Y. Ho, K. B. Sharpless, P. Taylor, V. V. Fokin
Generation Of Candidate Ligands For Nicotinic Acetylcholine Receptors Via In Situ Click Chemistry With A Soluble Acetylcholine Binding Protein Template.
J. Am. Chem. Soc. V. 134 6732 2012
PubMed-ID: 22394239 | Reference-DOI: 10.1021/JA3001858

Molecule 1 - SOLUBLE ACETYLCHOLINE RECEPTOR
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	HOMO SAPIENS
	Expression System Cell Line	:	HEK293S-GNT1-
	Expression System Common	:	HUMAN
	Expression System Plasmid	:	PFLAG-CMV3
	Expression System Taxid	:	9606
	Expression System Vector Type	:	PLASMID
	Organism Common	:	CALIFORNIA SEA HARE
	Organism Scientific	:	APLYSIA CALIFORNICA
	Organism Taxid	:	6500
	Synonym	:	AC-ACHBP

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 11)

No.	Name	Count	Type	Full Name
1	0J0	5	Ligand/Ion	(3-EXO)-8,8-DIMETHYL-3-(4-{[(1-METHYL-2-OXO-1,2-DIHYDROQUINOLIN-4-YL)OXY]METHYL}-1H-1,2,3-TRIAZOL-1-YL)-8-AZONIABICYCLO[3.2.1]OCTANE
2	BMA	1	Ligand/Ion	BETA-D-MANNOSE
3	MAN	2	Ligand/Ion	ALPHA-D-MANNOSE
4	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:70 , ASN A:74	BINDING SITE FOR RESIDUE NAG A 301
02	AC2	SOFTWARE	TYR A:93 , SER A:146 , TRP A:147	BINDING SITE FOR RESIDUE 0J0 A 302
03	AC3	SOFTWARE	TYR B:93 , TRP B:147 , TYR B:188 , TYR B:195	BINDING SITE FOR RESIDUE 0J0 B 300
04	AC4	SOFTWARE	GLN B:57 , ARG B:79 , VAL B:108 , MET B:116 , ILE B:118 , HOH B:406 , TYR C:93 , SER C:146 , TRP C:147 , VAL C:148 , TYR C:188 , CYS C:190 , CYS C:191 , PRO C:192 , GLU C:193 , TYR C:195	BINDING SITE FOR RESIDUE 0J0 C 300
05	AC5	SOFTWARE	GLN C:57 , ARG C:79 , VAL C:108 , MET C:116 , ILE C:118 , SER D:146 , TRP D:147 , CYS D:190 , CYS D:191 , PRO D:192 , GLU D:193 , TYR D:195	BINDING SITE FOR RESIDUE 0J0 D 300
06	AC6	SOFTWARE	ASN E:74 , NAG E:302	BINDING SITE FOR RESIDUE NAG E 301
07	AC7	SOFTWARE	NAG E:301 , BMA E:303 , MAN E:305	BINDING SITE FOR RESIDUE NAG E 302
08	AC8	SOFTWARE	ASN B:70 , NAG E:302 , MAN E:304 , MAN E:305	BINDING SITE FOR RESIDUE BMA E 303
09	AC9	SOFTWARE	ARG B:8 , GLU B:71 , GLU B:136 , BMA E:303	BINDING SITE FOR RESIDUE MAN E 304
10	BC1	SOFTWARE	NAG E:302 , BMA E:303	BINDING SITE FOR RESIDUE MAN E 305
11	BC2	SOFTWARE	TYR D:55 , GLN D:57 , VAL D:108 , MET D:116 , ILE D:118 , HOH D:415 , SER E:146 , TRP E:147 , VAL E:148 , TYR E:188 , CYS E:190 , CYS E:191 , PRO E:192 , GLU E:193 , TYR E:195	BINDING SITE FOR RESIDUE 0J0 E 306

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 4DBM)

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

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

(no "Exon" information available for 4DBM)

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
                                    23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223 
         Q8WSF8_APLCA    14 VGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d4dbma_ A: automated matches                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh.............eeeeeeeeeeeeeeee....eeeeeeeeeeeeeeeeee..........eeeee.hhh....eee.......ee....eeeee.eeeeee..eeeeeee...........eeeeeeeee.......eeee................eeeeeeeeeeeee........eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4dbm A  -3 DDKLHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     6        16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206

Chain B from PDB  Type:PROTEIN  Length:209
 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 d4dbmb_ B: 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
                 4dbm B  -2 DKLHSQANLMRLKSDLFNR-PMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     7        |-|       27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                             16 |                                                                                                                                                                                             
                                               18

Chain C from PDB  Type:PROTEIN  Length:206
 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 d4dbmc_ C: automat    ed 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................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dbm C  -2 DKLHSQANLMRLKSDLFN----YPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     7       | -  |     27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                            15   20

Chain D from PDB  Type:PROTEIN  Length:213
 aligned with Q8WSF8_APLCA | Q8WSF8 from UniProtKB/TrEMBL  Length:236

    Alignment length:216
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218      
         Q8WSF8_APLCA     9 LLVACVGQAHSQANLMRLKSDLFNRSPMYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 224
               SCOP domains d4dbmd_ D: automated mat   ches                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhh.---..........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
                 4dbm D  -8 DYKDDDDKLHSQANLMRLKSDLFN---MYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     1        11   |   |21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201      
                                                  15  19

Chain E from PDB  Type:PROTEIN  Length:209
 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 d4dbme_ E: 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................eeeeeeeeeeeeeee..eeeeeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4dbm E  -2 DKLHSQANLMRLKSDLFNRS-MYPGPTKDDPLTVTLGFTLQDIVKADSSTNEVDLVYYEQQRWKLNSLMWDPNEYGNITDFRTSAADIWTPDITAYSSTRPVQVLSPQIAVVTHDGSVMFIPAQRLSFMCDPTGVDSEEGATCAVKFGSWVYSGFEIDLKTDTDQVDLSSYYASSKYEILSATQTRQVQHYSCCPEPYIDVNLVVKFRER 207
                                     7        17 |      27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207
                                              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	d4dbma_	A:
1b	d4dbmb_	B:
1c	d4dbmc_	C:
1d	d4dbmd_	D:
1e	d4dbme_	E:

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

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

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
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 11)

Sites (11, 11)

SS Bonds (10, 10)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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