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(-) Description

Title :  CHOLERA TOXIN B-PENTAMER COMPLEXED WITH GM1 PENTASACCHARIDE
 
Authors :  E. A. Merritt, W. G. J. Hol
Date :  24 Mar 98  (Deposition) - 12 Aug 98  (Release) - 28 Jul 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym./Biol. Unit :  D,E,F,G,H
Keywords :  Toxin, Toxin/Receptor Complex, Pentasaccharide (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. A. Merritt, P. Kuhn, S. Sarfaty, J. L. Erbe, R. K. Holmes, W. G. Hol
The 1. 25 A Resolution Refinement Of The Cholera Toxin B-Pentamer: Evidence Of Peptide Backbone Strain At The Receptor-Binding Site.
J. Mol. Biol. V. 282 1043 1998
PubMed-ID: 9753553  |  Reference-DOI: 10.1006/JMBI.1998.2076
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CHOLERA TOXIN
    Chains: D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: B-PENTAMER
    Mutation: YES
    Organism Scientific: VIBRIO CHOLERAE
    Organism Taxid: 666
    Other Details: RECEPTOR BINDING SITE ON EACH MONOMER OCCUPIED BY GM1 PENTASACCHARIDE
    Strain: OGAWA 41 (CLASSICAL BIOTYPE)

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : DEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 32)

Asymmetric/Biological Unit (7, 32)
No.NameCountTypeFull Name
1BGC3Ligand/IonBETA-D-GLUCOSE
2GAL10Ligand/IonBETA-D-GALACTOSE
3GLC2Ligand/IonALPHA-D-GLUCOSE
4MES2Ligand/Ion2-(N-MORPHOLINO)-ETHANESULFONIC ACID
5NGA5Ligand/IonN-ACETYL-D-GALACTOSAMINE
6SIA5Ligand/IonO-SIALIC ACID
7UNX5Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (27, 27)

Asymmetric Unit (27, 27)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLU D:51 , GLN D:56 , HIS D:57 , GLN D:61 , TRP D:88 , ASN D:90 , LYS D:91 , NGA D:105 , HOH D:7002 , HOH D:7007BINDING SITE FOR RESIDUE GAL D 104
02AC2SOFTWAREGLN D:56 , ILE D:58 , GAL D:104 , GAL D:106 , SIA D:108 , HOH D:7001 , HOH D:7005 , HOH D:7007 , HOH D:7008 , HOH D:9318 , HOH H:9436BINDING SITE FOR RESIDUE NGA D 105
03AC3SOFTWARELYS D:34 , NGA D:105 , GLC D:107 , SIA D:108 , ILE H:58 , NGA H:105 , HOH H:9436 , HOH H:9799BINDING SITE FOR RESIDUE GAL D 106
04AC4SOFTWAREGAL D:106 , NGA H:105 , GAL H:106 , HOH H:9799BINDING SITE FOR RESIDUE GLC D 107
05AC5SOFTWAREGLU D:11 , TYR D:12 , HIS D:13 , ILE D:58 , NGA D:105 , GAL D:106 , HOH D:7002 , HOH D:7003 , HOH D:7005 , HOH D:9617 , GLY E:33BINDING SITE FOR RESIDUE SIA D 108
06AC6SOFTWAREGLU E:51 , GLN E:56 , GLN E:61 , TRP E:88 , ASN E:90 , LYS E:91 , NGA E:105 , HOH E:7101 , HOH E:7102 , HOH E:7105 , HOH E:7107BINDING SITE FOR RESIDUE GAL E 104
07AC7SOFTWAREGLN E:56 , ILE E:58 , GAL E:104 , GAL E:106 , SIA E:108 , HOH E:7108 , HOH E:9787 , HOH E:9815 , HOH F:9661BINDING SITE FOR RESIDUE NGA E 105
08AC8SOFTWARENGA E:105 , BGC E:107 , SIA E:108 , HOH E:9334 , HOH E:9451 , HOH E:9618 , HOH F:9232 , HOH G:9410BINDING SITE FOR RESIDUE GAL E 106
09AC9SOFTWAREASP D:7 , HOH D:9402 , GAL E:106 , HOH E:9351 , HOH E:9451 , HOH F:9777 , GLY G:54 , SER G:55 , GLN G:56 , HOH G:9295 , HOH G:9410BINDING SITE FOR RESIDUE BGC E 107
10BC1SOFTWAREGLU E:11 , TYR E:12 , HIS E:13 , ILE E:58 , NGA E:105 , GAL E:106 , HOH E:7102 , HOH E:7103 , HOH E:7105 , HOH E:9437 , HOH E:9729 , HOH E:9815 , GLY F:33BINDING SITE FOR RESIDUE SIA E 108
11BC2SOFTWAREGLU F:51 , GLN F:56 , HIS F:57 , GLN F:61 , TRP F:88 , ASN F:90 , LYS F:91 , NGA F:105 , HOH F:7201 , HOH F:7202 , HOH F:7205 , HOH F:7207BINDING SITE FOR RESIDUE GAL F 104
12BC3SOFTWAREASN F:14 , GLN F:56 , HIS F:57 , ILE F:58 , GAL F:104 , GAL F:106 , SIA F:108 , HOH F:7201 , HOH F:7205 , HOH F:7207 , HOH F:7208BINDING SITE FOR RESIDUE NGA F 105
13BC4SOFTWAREHIS F:13 , NGA F:105 , GLC F:107 , SIA F:108BINDING SITE FOR RESIDUE GAL F 106
14BC5SOFTWAREGAL F:106BINDING SITE FOR RESIDUE GLC F 107
15BC6SOFTWAREGLU F:11 , TYR F:12 , HIS F:13 , ILE F:58 , NGA F:105 , GAL F:106 , HOH F:7202 , HOH F:7203 , HOH F:7205 , GLY G:33BINDING SITE FOR RESIDUE SIA F 108
16BC7SOFTWAREGLU G:51 , GLN G:56 , HIS G:57 , GLN G:61 , TRP G:88 , ASN G:90 , LYS G:91 , NGA G:105 , HOH G:7301 , HOH G:7302 , HOH G:7305 , HOH G:7307BINDING SITE FOR RESIDUE GAL G 104
17BC8SOFTWAREHIS D:18 , HOH D:9194 , HOH D:9306 , GLN G:56 , ILE G:58 , GAL G:104 , GAL G:106 , SIA G:108 , HOH G:7301 , HOH G:7305 , HOH G:7307 , HOH G:7308BINDING SITE FOR RESIDUE NGA G 105
18BC9SOFTWAREGLN D:16 , HIS D:18 , HOH D:9251 , HIS G:13 , NGA G:105 , BGC G:107 , SIA G:108 , HOH G:9720BINDING SITE FOR RESIDUE GAL G 106
19CC1SOFTWAREHIS D:18 , ALA D:46 , THR D:47 , HOH D:9132 , GAL G:106 , HOH G:9581 , HOH G:9713 , HOH G:9733 , HOH H:9375BINDING SITE FOR RESIDUE BGC G 107
20CC2SOFTWAREGLU G:11 , TYR G:12 , HIS G:13 , ILE G:58 , NGA G:105 , GAL G:106 , HOH G:7302 , HOH G:7303 , HOH G:7305 , HOH G:9552 , HOH G:9634BINDING SITE FOR RESIDUE SIA G 108
21CC3SOFTWAREASN D:21 , ASP D:22 , LYS D:43 , LYS D:81 , HOH D:9068 , HOH D:9397 , ASN G:89 , LYS G:91 , THR G:92 , ARG G:94 , LYS H:43 , HOH H:9781BINDING SITE FOR RESIDUE MES G 6001
22CC4SOFTWAREASN E:21 , ASP E:22 , LYS E:81 , LYS G:43 , ASN H:89 , ASN H:90 , LYS H:91 , THR H:92 , ARG H:94 , HOH H:9257BINDING SITE FOR RESIDUE MES G 6002
23CC5SOFTWAREGLU H:51 , GLN H:56 , HIS H:57 , GLN H:61 , TRP H:88 , ASN H:90 , LYS H:91 , NGA H:105 , HOH H:7401 , HOH H:7402 , HOH H:7405 , HOH H:7407BINDING SITE FOR RESIDUE GAL H 104
24CC6SOFTWAREGAL D:106 , GLC D:107 , HIS E:18 , GLN H:56 , GAL H:104 , GAL H:106 , SIA H:108 , HOH H:7407 , HOH H:7408 , HOH H:9538 , HOH H:9799BINDING SITE FOR RESIDUE NGA H 105
25CC7SOFTWAREGLC D:107 , GLN E:16 , HIS H:13 , NGA H:105 , BGC H:107 , SIA H:108BINDING SITE FOR RESIDUE GAL H 106
26CC8SOFTWAREHIS E:18 , ALA E:46 , THR E:47 , ARG E:94 , HOH E:9269 , HIS H:13 , GAL H:106 , HOH H:9154 , HOH H:9361 , HOH H:9717BINDING SITE FOR RESIDUE BGC H 107
27CC9SOFTWAREGLU H:11 , TYR H:12 , HIS H:13 , ILE H:58 , NGA H:105 , GAL H:106 , HOH H:7402 , HOH H:7403 , HOH H:7405 , HOH H:9814BINDING SITE FOR RESIDUE SIA H 108

(-) SS Bonds  (5, 5)

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

(-) Cis Peptide Bonds  (5, 5)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3CHB)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3CHB)

(-) Exons   (0, 0)

(no "Exon" information available for 3CHB)

(-) Sequences/Alignments

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 d3chbd_ D: Cholera toxin                                                                                SCOP domains
               CATH domains 3chbD00 D:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....eeeeeeee...eeeee......eeeee.....eeee..........hhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3chb D   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPRAIAAISMAN 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 d3chbe_ E: Cholera toxin                                                                                SCOP domains
               CATH domains 3chbE00 E:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....eeeeeeee...eeeee......eeeee.....eeee..........hhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3chb E   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPRAIAAISMAN 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 d3chbf_ F: Cholera toxin                                                                                SCOP domains
               CATH domains 3chbF00 F:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....eeeeeeee...eeeee......eeeee.....eeee..........hhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3chb F   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPRAIAAISMAN 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 d3chbg_ G: Cholera toxin                                                                                SCOP domains
               CATH domains 3chbG00 G:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....eeeeeeee...eeeee......eeeee.....eeee..........hhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3chb G   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPRAIAAISMAN 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 d3chbh_ H: Cholera toxin                                                                                SCOP domains
               CATH domains 3chbH00 H:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh.....eeeeeeee...eeeee......eeeee.....eeee..........hhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 3chb H   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPRAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100
   Legend:   → Mismatch (orange background)
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  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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 5)

Asymmetric/Biological Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3CHB)

(-) Gene Ontology  (9, 9)

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.

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        CHTB_VIBCH | P01556: 1chp 1chq 1ct1 1fgb 1g8z 1jr0 1md2 1rcv 1rd9 1rdp 1rf2 1s5b 1s5c 1s5d 1s5e 1s5f 1xtc 2chb 3efx 5elc 5ele 5elf 5lzg 5lzj

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3CHB)