1PZJ - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   CHOLERA TOXIN B-PENTAMER COMPLEXED WITH NITROPHENYL GALACTOSIDE 5

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 :   1.46

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 (2, 5)

No.	Name	Count	Type	Full Name
1	15B	3	Ligand/Ion	N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-NITRO-5-(GALACTOPYRANOSYL)-BETA-BENZAMIDE
2	J15	2	Ligand/Ion	N-{3-[4-(3-AMINO-PROPYL)-PIPERAZIN-1-YL]-PROPYL}-3-NITRO-5-(GALACTOPYRANOSYL)-ALPHA-BENZAMIDE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLU D:11 , LYS D:34 , GLU D:51 , GLN D:56 , HIS D:57 , GLN D:61 , TRP D:88 , ASN D:90 , LYS D:91 , HOH D:1513 , HOH D:1515 , HOH D:1516 , HOH D:1520 , HOH D:1521 , HOH D:1608 , ILE H:58 , HOH H:1611	BINDING SITE FOR RESIDUE 15B 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:1488 , HOH E:1517 , HOH E:1596 , GLY F:33	BINDING SITE FOR RESIDUE J15 E 105
3	AC3	SOFTWARE	GLU F:11 , 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:1491 , HOH F:1636 , GLY G:33 , ARG G:35	BINDING SITE FOR RESIDUE J15 F 106
4	AC4	SOFTWARE	GLN D:16 , GLU G:11 , 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:1492 , HOH G:1494 , HOH G:1509 , HOH G:1527 , GLY H:33 , ARG H:35 , HOH H:1338	BINDING SITE FOR RESIDUE 15B G 107
5	AC5	SOFTWARE	GLY D:33 , LYS D:34 , ARG D:35 , GLN E:16 , HOH E:1093 , 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:1382 , HOH H:1483 , HOH H:1512 , HOH H:1650	BINDING SITE FOR RESIDUE 15B 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 1PZJ)

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

(no "Exon" information available for 1PZJ)

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 d1pzjd_ D: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzjD00 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
                 1pzj 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 d1pzje_ E: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzjE00 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
                 1pzj 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 d1pzjf_ F: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzjF00 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
                 1pzj 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 d1pzjg_ G: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzjG00 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
                 1pzj 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 d1pzjh_ H: Cholera toxin                                                                                SCOP domains
               CATH domains 1pzjH00 H: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
                 1pzj 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	d1pzjd_	D:
1b	d1pzje_	E:
1c	d1pzjf_	F:
1d	d1pzjg_	G:
1e	d1pzjh_	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	1pzjD00	D:1-103
1b	1pzjE00	E:1-103
1c	1pzjF00	F:1-103
1d	1pzjG00	G:1-103
1e	1pzjH00	H:1-103

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

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
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	Cis Peptide Bonds
		Thr D:92 - Pro D:93	[ RasMol ]
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		Thr G:92 - Pro G:93	[ RasMol ]
		Thr H:92 - Pro H:93	[ RasMol ]

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	1pzj
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	Q57193_VIBCL \| Q57193
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	Q57193_VIBCL \| Q57193	:	5eld 5lzh
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	Q57193_VIBCL \| Q57193	:	1eei 1llr 1pzk 5elb

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 5)

Sites (5, 5)

SS Bonds (5, 5)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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