1PZK - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CHOLERA TOXIN B-PENTAMER COMPLEXED WITH N-ACYL PHENYL GALACTOSIDE 9H

Authors :   D. D. Mitchell, J. C. Pickens, K. Korotkov, E. Fan, W. G. J. Hol

Date :   11 Jul 03 (Deposition) - 09 Mar 04 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.35

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

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

Reference :   D. D. Mitchell, J. C. Pickens, K. Korotkov, E. Fan, W. G. J. Hol
3, 5-Substituted Phenyl Galactosides As Leads In Designing Effective Cholera Toxin Antagonists; Synthesis And Crystallographic Studies
Bioorg. Med. Chem. V. 12 907 2004
PubMed-ID: 14980603 | Reference-DOI: 10.1016/J.BMC.2003.12.019
(for further references see the PDB file header)

Molecule 1 - CHOLERA TOXIN B SUBUNIT
	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	:	CAA41591
	Organism Scientific	:	VIBRIO CHOLERAE
	Organism Taxid	:	666
	Synonym	:	CTB

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

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 5)

No.	Name	Count	Type	Full Name
1	J12	5	Ligand/Ion	N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-(2-THIOPHEN-2-YL-ACETYLAMINO)-5-(3,4,5-TRIHYDROXY-6-HYDROXYMETHYL-TETRAHYDRO-PYRAN-2-YLOXY)-BENZAMIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH D:1431 , HIS G:13 , GLU G:51 , GLN G:56 , GLN G:61 , TRP G:88 , ASN G:90 , LYS G:91 , HOH G:1466 , HOH G:1467 , HOH G:1477 , HOH G:1627	BINDING SITE FOR RESIDUE J12 G 104
2	AC2	SOFTWARE	TYR D:12 , HIS D:13 , GLU D:51 , GLN D:56 , HIS D:57 , GLN D:61 , TRP D:88 , ASN D:90 , LYS D:91 , HOH D:1576 , HOH D:1577 , HOH D:1578 , HOH D:1586 , HOH E:1480	BINDING SITE FOR RESIDUE J12 D 105
3	AC3	SOFTWARE	TYR E:12 , HIS E:13 , GLU E:51 , GLN E:56 , GLN E:61 , TRP E:88 , ASN E:90 , LYS E:91 , HOH E:1591 , HOH E:1592 , HOH E:1624 , HOH F:1479	BINDING SITE FOR RESIDUE J12 E 106
4	AC4	SOFTWARE	HIS F:13 , GLU F:51 , GLN F:56 , HIS F:57 , GLN F:61 , TRP F:88 , ASN F:90 , LYS F:91 , HOH F:1605 , HOH F:1606 , HOH F:1625 , HOH G:1478	BINDING SITE FOR RESIDUE J12 F 107
5	AC5	SOFTWARE	LYS D:34 , ARG D:35 , HOH D:1572 , HOH E:1456 , GLU H:11 , TYR H:12 , HIS H:13 , GLU H:51 , GLN H:56 , HIS H:57 , GLN H:61 , TRP H:88 , ASN H:90 , LYS H:91 , HOH H:1481 , HOH H:1485 , HOH H:1570 , HOH H:1571	BINDING SITE FOR RESIDUE J12 H 108

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 1PZK)

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

(no "Exon" information available for 1PZK)

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 Q57193_VIBCL | Q57193 from UniProtKB/TrEMBL  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
         Q57193_VIBCL    22 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1pzkd_ D: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzkD00 D: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
                 1pzk D   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain E from PDB  Type:PROTEIN  Length:103
 aligned with Q57193_VIBCL | Q57193 from UniProtKB/TrEMBL  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
         Q57193_VIBCL    22 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1pzke_ E: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzkE00 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
                 1pzk E   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain F from PDB  Type:PROTEIN  Length:103
 aligned with Q57193_VIBCL | Q57193 from UniProtKB/TrEMBL  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
         Q57193_VIBCL    22 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1pzkf_ F: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzkF00 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
                 1pzk F   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain G from PDB  Type:PROTEIN  Length:103
 aligned with Q57193_VIBCL | Q57193 from UniProtKB/TrEMBL  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
         Q57193_VIBCL    22 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1pzkg_ G: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzkG00 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
                 1pzk G   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100

Chain H from PDB  Type:PROTEIN  Length:103
 aligned with Q57193_VIBCL | Q57193 from UniProtKB/TrEMBL  Length:124

    Alignment length:103
                                    31        41        51        61        71        81        91       101       111       121   
         Q57193_VIBCL    22 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 124
               SCOP domains d1pzkh_ H: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzkH00 H:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeeee...eeeee......eeeee.....eeee.........hhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1pzk 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	d1pzkd_	D:
1b	d1pzke_	E:
1c	d1pzkf_	F:
1d	d1pzkg_	G:
1e	d1pzkh_	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	1pzkD00	D:1-103
1b	1pzkE00	E:1-103
1c	1pzkF00	F:1-103
1d	1pzkG00	G:1-103
1e	1pzkH00	H:1-103

(no "Pfam Domain" information available for 1PZK)

Asymmetric/Biological Unit(hide GO term definitions)

Chain D,E,F,G,H (Q57193_VIBCL | Q57193)

biological process
	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.
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.

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
		J12	[ 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 ]

	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
	1pzk
		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
	Q57193_VIBCL \| Q57193
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/TrEMBL

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
	Q57193_VIBCL \| Q57193
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	Q57193_VIBCL \| Q57193	:	5eld 5lzh
UniProtKB/TrEMBL
	Q57193_VIBCL \| Q57193	:	1eei 1llr 1pzj 5elb

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

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 (0, 0)

Gene Ontology (2, 2)

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