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Title :   CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV4

Authors :   J. C. Pickens, D. D. Mitchell, J. Liu, X. Tan, Z. Zhang, C. L. Verlinde, W. G. Hol, E. Fan

Date :   07 Nov 03 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

Chains :   Asym./Biol. Unit : D,E,F,G,H

Keywords :   Bivalent, Cholera, Toxin, Pentamer, Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. C. Pickens, D. D. Mitchell, J. Liu, X. Tan, Z. Zhang, C. L. Verlinde, W. G. Hol, E. Fan
Nonspanning Bivalent Ligands As Improved Surface Receptor Binding Inhibitors Of The Cholera Toxin B Pentamer.
Chem. Biol. V. 11 1205 2004
PubMed-ID: 15380181 | Reference-DOI: 10.1016/J.CHEMBIOL.2004.06.008
(for further references see the PDB file header)

Molecule 1 - CHOLERA TOXIN B PROTEIN (CTB)
	Chains	:	D, E, F, G, H
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PBAD
	Expression System Strain	:	TOP10
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	CTXB
	Organism Scientific	:	VIBRIO CHOLERAE
	Organism Taxid	:	666

		1	2	3	4	5
Asymmetric/Biological Unit	:	D	E	F	G	H

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	BV4	5	Ligand/Ion	1,3-BIS-([3-[3-[3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYLAMINO-3,4-DIOXO-CYCLOBUTENYL]-AMINO-PROPOXY-ETHOXY-ETHOXY]-PROPYL-]AMINO-CARBONYLOXY)-2-AMINO-PROPANE
2	PGE	1	Ligand/Ion	TRIETHYLENE GLYCOL
3	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (7, 7)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	TYR D:12 , GLU D:51 , GLN D:56 , HIS D:57 , GLN D:61 , TRP D:88 , ASN D:90 , LYS D:91 , HOH D:1133 , HOH D:1352 , HOH D:1481 , GLY E:33	BINDING SITE FOR RESIDUE BV4 D 104
2	AC2	SOFTWARE	TYR E:12 , GLU E:51 , GLN E:56 , GLN E:61 , TRP E:88 , ASN E:90 , LYS E:91 , HOH E:1262 , HOH E:1480 , GLY F:33	BINDING SITE FOR RESIDUE BV4 E 105
3	AC3	SOFTWARE	TYR F:12 , GLU F:51 , GLN F:56 , HIS F:57 , GLN F:61 , TRP F:88 , ASN F:90 , LYS F:91 , HOH F:1049 , HOH F:1152 , GLY G:33	BINDING SITE FOR RESIDUE BV4 F 106
4	AC4	SOFTWARE	TYR G:12 , GLU G:51 , GLN G:56 , HIS G:57 , GLN G:61 , TRP G:88 , ASN G:90 , LYS G:91 , HOH G:1018 , HOH G:1137 , HOH G:1261 , GLY H:33	BINDING SITE FOR RESIDUE BV4 G 107
5	AC5	SOFTWARE	GLY D:33 , TYR H:12 , GLU H:51 , GLN H:56 , HIS H:57 , GLN H:61 , TRP H:88 , ASN H:90 , LYS H:91 , HOH H:1048 , HOH H:1150 , HOH H:1346 , HOH H:1479	BINDING SITE FOR RESIDUE BV4 H 108
6	AC6	SOFTWARE	ARG D:35 , ASN F:14 , ASN F:89 , ASN F:90 , THR H:1 , PRO H:2 , ASP H:7 , GLU H:11 , HOH H:1075 , HOH H:1496	BINDING SITE FOR RESIDUE TRS H 109
7	AC7	SOFTWARE	LYS D:91 , THR D:92 , ASN F:89 , ASN F:90 , LYS F:91 , THR F:92 , THR H:1 , HOH H:1472	BINDING SITE FOR RESIDUE PGE H 110

Asymmetric/Biological Unit

No.	Residues
1	D:9	-	D:86
2	E:9	-	E:86
3	F:9	-	F:86
4	G:9	-	G:86
5	H:9	-	H:86

Asymmetric/Biological Unit

No.	Residues
1	Thr D:92	-	Pro D:93
2	Thr E:92	-	Pro E:93
3	Thr F:92	-	Pro F:93
4	Thr G:92	-	Pro G:93
5	Thr H:92	-	Pro H:93

(no "SAP(SNP)/Variant" information available for 1RF2)

(no "PROSITE Motif" information available for 1RF2)

(no "Exon" information available for 1RF2)

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 D from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1rf2d_ D: Cholera toxin                                                                                SCOP domains
               CATH domains 1rf2D00 D:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeeee..eeeee.......eeee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh.eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1rf2 D   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain E from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1rf2e_ E: Cholera toxin                                                                                SCOP domains
               CATH domains 1rf2E00 E:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee.......eeee.....eeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1rf2 E   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain F from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1rf2f_ F: Cholera toxin                                                                                SCOP domains
               CATH domains 1rf2F00 F:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeeee...eeeee.......eeee.....eeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1rf2 F   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain G from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1rf2g_ G: Cholera toxin                                                                                SCOP domains
               CATH domains 1rf2G00 G:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee......eeeee.....eeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1rf2 G   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain H from PDB  Type:PROTEIN  Length:103
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1rf2h_ H: Cholera toxin                                                                                SCOP domains
               CATH domains 1rf2H00 H:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
           Pfam domains (1) Enterotoxin_b-1rf2H01 H:1-102                                                                         - Pfam domains (1)
           Pfam domains (2) Enterotoxin_b-1rf2H02 H:1-102                                                                         - Pfam domains (2)
           Pfam domains (3) Enterotoxin_b-1rf2H03 H:1-102                                                                         - Pfam domains (3)
           Pfam domains (4) Enterotoxin_b-1rf2H04 H:1-102                                                                         - Pfam domains (4)
           Pfam domains (5) Enterotoxin_b-1rf2H05 H:1-102                                                                         - Pfam domains (5)
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee......eeeee.....eeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1rf2 H   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

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: OB-fold (1179)

Superfamily: Bacterial enterotoxins (188)

Family: Bacterial AB5 toxins, B-subunits (85)

Protein domain: Cholera toxin (24)

Vibrio cholerae [TaxId: 666] (24)

1a	d1rf2d_	D:
1b	d1rf2e_	E:
1c	d1rf2f_	F:
1d	d1rf2g_	G:
1e	d1rf2h_	H:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: OB fold (Dihydrolipoamide Acetyltransferase, E2P) (1040)

Homologous Superfamily: [code=2.40.50.110, no name defined] (136)

Vibrio cholerae. Organism_taxid: 666. (15)

1a	1rf2D00	D:1-103
1b	1rf2E00	E:1-103
1c	1rf2F00	F:1-103
1d	1rf2G00	G:1-103
1e	1rf2H00	H:1-103

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Enterotoxin_b] (23)

Family: Enterotoxin_b (23)

Vibrio cholerae (11)

1a	Enterotoxin_b-1rf2H01	H:1-102
1b	Enterotoxin_b-1rf2H02	H:1-102
1c	Enterotoxin_b-1rf2H03	H:1-102
1d	Enterotoxin_b-1rf2H04	H:1-102
1e	Enterotoxin_b-1rf2H05	H:1-102

Asymmetric/Biological Unit(hide GO term definitions)

Chain D,E,F,G,H (CHTB_VIBCH | P01556)

molecular function
	GO:0046812	host cell surface binding	Interacting selectively and non-covalently with the surface of a host cell.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0031640	killing of cells of other organism	Any process in an organism that results in the killing of cells of another organism, including in some cases the death of the other organism. Killing here refers to the induction of death in one cell by another cell, not cell-autonomous death due to internal or other environmental conditions.
	GO:0009405	pathogenesis	The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
	GO:0006471	protein ADP-ribosylation	The transfer, from NAD, of ADP-ribose to protein amino acids.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0033644	host cell membrane	Double layer of lipid molecules as it encloses host cells, and, in eukaryotes, many organelles; may be a single or double lipid bilayer; also includes associated proteins. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0020002	host cell plasma membrane	The plasma membrane surrounding a host cell.
	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
		Thr D:92 - Pro D:93	[ RasMol ]
		Thr E:92 - Pro E:93	[ RasMol ]
		Thr F:92 - Pro F:93	[ RasMol ]
		Thr G:92 - Pro G:93	[ RasMol ]
		Thr H:92 - Pro H:93	[ RasMol ]

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	1rf2
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1rcv	CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV1
1rd9	CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV2
1rdp	CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV3

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

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