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(-) Description

Title :  CHOLERA HOLOTOXIN, CRYSTAL FORM 2
 
Authors :  C. J. O'Neal, E. I. Amaya, M. G. Jobling, R. K. Holmes, W. G. Hol
Date :  20 Jan 04  (Deposition) - 06 Apr 04  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,D,E,F,G,H
Biol. Unit 1:  A,D,E,F,G,H  (1x)
Biol. Unit 2:  A (1x),D (1x),E (1x),F (1x),G (1x),H (1x)
Keywords :  Cholera Toxin, Heat-Labile Enterotoxin, Adp Ribose Transferases, Ab5 Toxins, Transferase, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. J. O'Neal, E. I. Amaya, M. G. Jobling, R. K. Holmes, W. G. Hol
Crystal Structures Of An Intrinsically Active Cholera Toxin Mutant Yield Insight Into The Toxin Activation Mechanism
Biochemistry V. 43 3772 2004
PubMed-ID: 15049684  |  Reference-DOI: 10.1021/BI0360152

(-) Compounds

Molecule 1 - CHOLERA ENTEROTOXIN, A CHAIN
    ChainsA
    EC Number2.4.2.36
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPARCT5
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCTXA, TOXA, VC1457
    Organism ScientificVIBRIO CHOLERAE
    Organism Taxid666
    SynonymNAD(+)--DIPHTHAMIDE ADP- RIBOSYLTRANSFERASE, CHOLERA ENTEROTOXIN A SUBUNIT
 
Molecule 2 - CHOLERA TOXIN B PROTEIN (CTB)
    ChainsD, E, F, G, H
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPARCT5
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneCTXB, TOXB, VC1456
    Organism ScientificVIBRIO CHOLERAE
    Organism Taxid666

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ADEFGH
Biological Unit 1 (1x)ADEFGH
Biological Unit 2 (1x)A (1x)D (1x)E (1x)F (1x)G (1x)H (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1GAL5Ligand/IonBETA-D-GALACTOSE
2NA1Ligand/IonSODIUM ION
Biological Unit 1 (1, 5)
No.NameCountTypeFull Name
1GAL5Ligand/IonBETA-D-GALACTOSE
2NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GAL-1Ligand/IonBETA-D-GALACTOSE
2NA-1Ligand/IonSODIUM ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN D:14 , GLU D:51 , GLN D:56 , HIS D:57 , GLN D:61 , TRP D:88 , ASN D:90BINDING SITE FOR RESIDUE GAL D 104
2AC2SOFTWAREGLU E:51 , GLN E:56 , HIS E:57 , GLN E:61 , ASN E:90 , LYS E:91BINDING SITE FOR RESIDUE GAL E 105
3AC3SOFTWAREGLU F:51 , GLN F:56 , HIS F:57 , GLN F:61 , ASN F:90 , LYS F:91BINDING SITE FOR RESIDUE GAL F 106
4AC4SOFTWAREGLU G:51 , GLN G:56 , HIS G:57 , GLN G:61 , TRP G:88 , ASN G:90BINDING SITE FOR RESIDUE GAL G 107
5AC5SOFTWAREGLU H:51 , GLN H:56 , HIS H:57 , GLN H:61 , TRP H:88 , ASN H:90 , LYS H:91BINDING SITE FOR RESIDUE GAL H 108
6AC6SOFTWAREASN A:1 , THR A:90 , TYR A:150 , LEU A:153 , HOH A:243BINDING SITE FOR RESIDUE NA A 241

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1A:187 -A:199
2D:9 -D:86
3E:9 -E:86
4F:9 -F:86
5G:9 -G:86
6H:9 -H:86

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:177 -Pro A:178
2Thr D:92 -Pro D:93
3Thr E:92 -Pro E:93
4Thr F:92 -Pro F:93
5Thr G:92 -Pro G:93
6Thr H:92 -Pro H:93

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1S5F)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1S5F)

(-) Exons   (0, 0)

(no "Exon" information available for 1S5F)

(-) Sequences/Alignments

Asymmetric 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 A from PDB  Type:PROTEIN  Length:224
 aligned with CHTA_VIBCH | P01555 from UniProtKB/Swiss-Prot  Length:258

    Alignment length:235
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248     
           CHTA_VIBCH    19 NDDKLYRADSRPPDEIKQSGGLMPRGQSEYFDRGTQMNINLYDHARGTQTGFVRHDDGYVSTSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDEQEVSALGGIPYSQIYGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGFPPEHRAWREEPWIHHAPPGCGNAPRSSMSNTCDEKTQSLGVKFLDEYQSKVKRQIFSGYQSDIDTHNR 253
               SCOP domains d1s5fa_ A: Cholera toxin                                                                                                                                                                                                                    SCOP domains
               CATH domains 1s5fA00 A:1-235 Heat-Labile Ente   rotoxin, subunit A                                                                                                                                                                                       CATH domains
               Pfam domains Enterotoxin_a-1s5fA01 A:1-235                                                                                                                                                                                                               Pfam domains
         Sec.struct. author ...eeeeee..hhhhhhhhhee..........---....hhhhhhhh...........eeee..hhhhhhhhhhhhh....eeeeeeee....eeehhhhhhhhh.hhhhh.eeee..ee...eeeeeeee..eeeeeeee....hhhhhh.....hhhhhhhhh.....hhhhhh.hhhhh.......--------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1s5f A   1 NDDKLYRADSRPPDEIKQSGGLMPRGQSEYFD---QMNINLYDHARGTQTGFVRHDDGYVSTSISLRSAHLVGQTILSGHSTYYIYVIATAPNMFNVNDVLGAYSPHPDEQEVSALGGIPYSQIYGWYRVHFGVLDEQLHRNRGYRDRYYSNLDIAPAADGYGLAGFPPEHRAWREEPWIHHAPPGCGN--------TCDEKTQSLGVKFLDEYQSKVKRQIFSGYQSDIDTHNR 235
                                    10        20        30 |   |  40        50        60        70        80        90       100       110       120       130       140       150       160       170       180        |-       200       210       220       230     
                                                          32  36                                                                                                                                                      189      198                                     

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 d1s5fd_ D: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5fD00 D:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeeee...eeeee.......eeee.....eeee.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5f 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 d1s5fe_ E: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5fE00 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.......hhhhhhhhhhhhhhhhhhhhhh..eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5f 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 d1s5ff_ F: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5fF00 F:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh...eeeeeeee...eeeee......eeeee.....eeee.........hhhhhhhhhhhhhhhhhhh...eeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5f F   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMAN 103
                                    10        20        30        40        50        60        70        80        90       100   

Chain G from PDB  Type:PROTEIN  Length:102
 aligned with CHTB_VIBCH | P01556 from UniProtKB/Swiss-Prot  Length:124

    Alignment length:102
                                    31        41        51        61        71        81        91       101       111       121  
           CHTB_VIBCH    22 TPQNITDLCAEYHNTQIYTLNDKIFSYTESLAGKREMAIITFKNGAIFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMA 123
               SCOP domains d1s5fg_ G: Cholera toxin                                                                               SCOP domains
               CATH domains 1s5fG00 G:1-102  [code=2.40.50.110, no name defined]                                                   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhh....eeeeeeee...eeeee......eeeee.....eeee.........hhhhhhhhhhhhhhhhhh....eeeeeee.....eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------ Transcript
                 1s5f G   1 TPQNITDLCAEYHNTQIHTLNDKIFSYTESLAGKREMAIITFKNGATFQVEVPGSQHIDSQKKAIERMKDTLRIAYLTEAKVEKLCVWNNKTPHAIAAISMA 102
                                    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 d1s5fh_ H: Cholera toxin                                                                                SCOP domains
               CATH domains 1s5fH00 H:1-103  [code=2.40.50.110, no name defined]                                                    CATH domains
           Pfam domains (1) Enterotoxin_b-1s5fH01 H:1-102                                                                         - Pfam domains (1)
           Pfam domains (2) Enterotoxin_b-1s5fH02 H:1-102                                                                         - Pfam domains (2)
           Pfam domains (3) Enterotoxin_b-1s5fH03 H:1-102                                                                         - Pfam domains (3)
           Pfam domains (4) Enterotoxin_b-1s5fH04 H:1-102                                                                         - Pfam domains (4)
           Pfam domains (5) Enterotoxin_b-1s5fH05 H:1-102                                                                         - Pfam domains (5)
         Sec.struct. author ...hhhhhhhh...eeeeeeeee..eeeee.......eeee.....eeee.......hhhhhhhhhhhhhhhhhhhhh..eeeeeeee.....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------- Transcript
                 1s5f 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 '|'

 Classification and Annotation

(-) SCOP Domains  (2, 6)

Asymmetric Unit

(-) CATH Domains  (2, 6)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (2, 6)

Asymmetric Unit

(-) Gene Ontology  (14, 19)

Asymmetric Unit(hide GO term definitions)
Chain A   (CHTA_VIBCH | P01555)
molecular function
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    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).
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
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:0030819    positive regulation of cAMP biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
    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.

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
        CHTA_VIBCH | P015551s5b 1s5c 1s5d 1s5e 1xtc 2a5d 2a5f 2a5g
        CHTB_VIBCH | P015561chp 1chq 1ct1 1fgb 1g8z 1jr0 1md2 1rcv 1rd9 1rdp 1rf2 1s5b 1s5c 1s5d 1s5e 1xtc 2chb 3chb 3efx 5elc 5ele 5elf 5lzg 5lzj

(-) Related Entries Specified in the PDB File

1lta HEAT-LABILE ENTEROTOXIN COMPLEXED WITH GALACTOSE
1ltg HEAT-LABILE ENTEROTOXIN WITH AN A-SUBUNIT R7K MUTATION
1lts HEAT-LABILE ENTEROTOXIN
1xtc CHOLERA HOLOTOXIN