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(-) Description

Title :  STAPHYLOCOCCAL ENTEROTOXIN B COMPLEXED WITH GM3 TRISACCHARIDE
 
Authors :  S. Swaminathan, M. Sax
Date :  11 Oct 96  (Deposition) - 16 Jun 97  (Release) - 08 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Toxin, Superantigen, Seb, Sialyllactose, Complex, Enterotoxin, Signal (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Swaminathan, W. Furey, J. Pletcher, M. Sax
Residues Defining V Beta Specificity In Staphylococcal Enterotoxins.
Nat. Struct. Biol. V. 2 680 1995
PubMed-ID: 7552730  |  Reference-DOI: 10.1038/NSB0895-680
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - STAPHYLOCOCCAL ENTEROTOXIN B
    Cell Line: S2
    Chains: A
    Engineered: YES
    Expression System: STAPHYLOCOCCUS AUREUS
    Expression System Taxid: 1280
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Other Details: COMPLEXED WITH GM3 TRISACCHARIDE (3'- SIALYLLACTOSE)
    Synonym: SEB

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 3)

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1BGC1Ligand/IonBETA-D-GLUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:41 , SER A:52 , LYS A:54 , ASP A:62 , ASN A:63 , GLN A:106 , ASP A:108 , HOH A:333 , GAL A:401BINDING SITE FOR RESIDUE SIA A 400
2AC2SOFTWAREPRO A:4 , HOH A:346 , SIA A:400 , BGC A:402BINDING SITE FOR RESIDUE GAL A 401
3AC3SOFTWAREPRO A:4 , THR A:133 , HOH A:346 , HOH A:365 , GAL A:401BINDING SITE FOR RESIDUE BGC A 402
4SACUNKNOWNLYS A:54 , ASP A:62 , ASN A:63 , GLN A:106 , ASP A:108TRISACCHARIDE BINDING SITE.

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:93 -A:113

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1SE3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1SE3)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1STAPH_STREP_TOXIN_1PS00277 Staphylococcal enterotoxin/Streptococcal pyrogenic exotoxin signature 1.ETXB_STAAU142-151  1A:115-124
2STAPH_STREP_TOXIN_2PS00278 Staphyloccocal enterotoxin/Streptococcal pyrogenic exotoxin signature 2.ETXB_STAAU179-202  1A:152-175

(-) Exons   (0, 0)

(no "Exon" information available for 1SE3)

(-) 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 A from PDB  Type:PROTEIN  Length:239
 aligned with ETXB_STAAU | P01552 from UniProtKB/Swiss-Prot  Length:266

    Alignment length:239
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257         
           ETXB_STAAU    28 ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK 266
               SCOP domains d1se3a1 A:1-121 Staphylococcal enterotoxin B, SEB                                                                        d1se3a2 A:122-239 Staphylococcal enterotoxin B, SEB                                                                    SCOP domains
               CATH domains -1se3A02 A:2-31,A:128-231      1se3A01 A:32-121  [code=2.40.50.110, no name defined]                                     ------1se3A02 A:2-31,A:128-231  [code=3.10.20.120, no name defined]                                           -------- CATH domains
               Pfam domains ----------------------Stap_Strp_toxin-1se3A02 A:23-121                                                                   --------Stap_Strp_tox_C-1se3A01 A:130-235                                                                         ---- Pfam domains
         Sec.struct. author ............hhhhh...hhhhhhhhh...eeeeee.........eeee...........eeeee..hhhhhhhhh...eeeee........................eeeee..eee.........eeeeeeeee......eeeeee...eeehhhhhhhhhhhhhhhh.........eeeeeeeee....eeeee..........hhhhhhhh....eee....eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------STAPH_STRE---------------------------STAPH_STREP_TOXIN_2     ---------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1se3 A   1 ESQPDPKPDELHKSSKFTGLMENMKVLYDDNHVSAINVKSIDQFLYFDLIYSIKDTKLGNYDNVRVEFKNKDLADKYKDKYVDVFGANYYYQCYFSKKTNDINSHQTDKRKTCMYGGVTEHNGNQLDKYRSITVRVFEDGKNLLSFDVQTNKKKVTAQELDYLTRHYLVKNKKLYEFNNSPYETGYIKFIENENSFWYDMMPAPGDKFDQSKYLMMYNDNKMVDSKDVKIEVYLTTKKK 239
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230
   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (2, 2)

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

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: Ant-toxin_C (48)
(-)
Clan: no clan defined [family: Stap_Strp_toxin] (39)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ETXB_STAAU | P01552)
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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ETXB_STAAU | P01552: 1d5m 1d5x 1d5z 1d6e 1goz 1sbb 1se4 1seb 2seb 3gp7 3r8b 3seb 3w2d 4c56 4rgm 4rgn 4rgo

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1SE3)