1RD9 - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV2

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

Date :   05 Nov 03 (Deposition) - 26 Oct 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.44

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	BV2	5	Ligand/Ion	1,3-BIS-([3-(4-{3-[3-NITRO-5-(GALACTOPYRANOSYLOXY)-BENZOYLAMINO]-PROPYL}-PIPERAZIN-1-YL)-PROPYL-AMINO]-CARBONYLOXY)-2-AMINO-PROPANE
2	P6G	1	Ligand/Ion	HEXAETHYLENE 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:1198 , HOH D:1386 , GLY E:33 , HOH H:1334	BINDING SITE FOR RESIDUE BV2 D 104
2	AC2	SOFTWARE	GLU E:11 , TYR E:12 , GLU E:51 , GLN E:56 , HIS E:57 , GLN E:61 , TRP E:88 , ASN E:90 , LYS E:91 , HOH E:1151 , HOH E:1488 , GLY F:33 , ARG F:35	BINDING SITE FOR RESIDUE BV2 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:1479 , GLY G:33	BINDING SITE FOR RESIDUE BV2 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:1004 , HOH G:1333 , HOH G:1476 , GLY H:33	BINDING SITE FOR RESIDUE BV2 G 107
5	AC5	SOFTWARE	GLY D:33 , LYS D:34 , GLU H:11 , 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:1029 , HOH H:1269 , HOH H:1285 , HOH H:1490	BINDING SITE FOR RESIDUE BV2 H 108
6	AC6	SOFTWARE	ARG D:35 , ASN F:14 , ASN F:89 , ASN F:90 , THR H:1 , PRO H:2 , GLU H:11 , HOH H:1483	BINDING SITE FOR RESIDUE TRS H 109
7	AC7	SOFTWARE	LYS D:91 , THR D:92 , THR H:1 , HOH H:1471 , HOH H:1491	BINDING SITE FOR RESIDUE P6G 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 1RD9)

(no "PROSITE Motif" information available for 1RD9)

(no "Exon" information available for 1RD9)

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 d1rd9d_ D: Cholera toxin                                                                                SCOP domains
               CATH domains 1rd9D00 D:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee.......eeee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1rd9 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 d1rd9e_ E: Cholera toxin                                                                                SCOP domains
               CATH domains 1rd9E00 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
                 1rd9 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 d1rd9f_ F: Cholera toxin                                                                                SCOP domains
               CATH domains 1rd9F00 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
                 1rd9 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 d1rd9g_ G: Cholera toxin                                                                                SCOP domains
               CATH domains 1rd9G00 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
                 1rd9 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 d1rd9h_ H: Cholera toxin                                                                                SCOP domains
               CATH domains 1rd9H00 H:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
           Pfam domains (1) Enterotoxin_b-1rd9H01 H:1-102                                                                         - Pfam domains (1)
           Pfam domains (2) Enterotoxin_b-1rd9H02 H:1-102                                                                         - Pfam domains (2)
           Pfam domains (3) Enterotoxin_b-1rd9H03 H:1-102                                                                         - Pfam domains (3)
           Pfam domains (4) Enterotoxin_b-1rd9H04 H:1-102                                                                         - Pfam domains (4)
           Pfam domains (5) Enterotoxin_b-1rd9H05 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
                 1rd9 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	d1rd9d_	D:
1b	d1rd9e_	E:
1c	d1rd9f_	F:
1d	d1rd9g_	G:
1e	d1rd9h_	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	1rd9D00	D:1-103
1b	1rd9E00	E:1-103
1c	1rd9F00	F:1-103
1d	1rd9G00	G:1-103
1e	1rd9H00	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-1rd9H01	H:1-102
1b	Enterotoxin_b-1rd9H02	H:1-102
1c	Enterotoxin_b-1rd9H03	H:1-102
1d	Enterotoxin_b-1rd9H04	H:1-102
1e	Enterotoxin_b-1rd9H05	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
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		BV2	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		P6G	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TRS	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]

	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 ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1rd9
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	CHTB_VIBCH \| P01556
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	CHTB_VIBCH \| P01556
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1rcv	CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV1
1rdp	CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV3
1rf2	CHOLERA TOXIN B-PENTAMER COMPLEXED WITH BIVALENT NITROPHENOL-GALACTOSIDE LIGAND BV4

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 7)

Sites (7, 7)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 5)

CATH Domains (1, 5)

Pfam Domains (1, 5)

Gene Ontology (9, 9)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File