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(-) Description

Title :  MUTATED SHIGA-LIKE TOXIN B SUBUNIT (F30A/W34A) COMPLEXED WITH RECEPTOR GB3 ANALOGUE
 
Authors :  H. Ling, J. L. Brunton, R. J. Read
Date :  31 Aug 99  (Deposition) - 20 Sep 00  (Release) - 01 Sep 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.52
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Toxin, Receptor Binding, Protein-Carbohydrate Recognition, Ob-Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Ling, D. Bast, J. L. Brunton, R. J. Read
Identification Of The Primary Receptor Binding Site Of Shiga-Like Toxin B Subunits: Structures Of Mutated Shiga-Like Toxin I B-Pentamer With And Without Bound Carbohydrate
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN (SHIGA-LIKE TOXIN I SUBUNIT B)
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: RECEPTOR-BINDING DOMAIN
    Mutation: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 15)

Asymmetric/Biological Unit (3, 15)
No.NameCountTypeFull Name
1BGC5Ligand/IonBETA-D-GLUCOSE
2GAL5Ligand/IonBETA-D-GALACTOSE
3GLA5Ligand/IonALPHA D-GALACTOSE

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:131 , ASN A:132 , ARG A:133 , PHE A:163 , SER A:164 , GAL A:191 , HOH A:755 , HOH A:757 , ASP B:216 , HOH B:607BINDING SITE FOR RESIDUE GLA A 190
02AC2SOFTWARETHR A:154 , ASN A:155 , GLY A:162 , GLA A:190 , BGC A:192 , HOH A:724 , HOH A:740 , HOH A:875 , HOH A:945BINDING SITE FOR RESIDUE GAL A 191
03AC3SOFTWAREASN A:155 , GAL A:191 , HOH A:875 , HOH A:920 , HOH D:726BINDING SITE FOR RESIDUE BGC A 192
04AC4SOFTWARETHR B:231 , ASN B:232 , ARG B:233 , GLY B:262 , PHE B:263 , SER B:264 , GAL B:291 , HOH B:649 , HOH B:765 , HOH B:893 , ASP C:316BINDING SITE FOR RESIDUE GLA B 290
05AC5SOFTWARETHR B:254 , ASN B:255 , GLY B:262 , GLA B:290 , BGC B:292 , HOH B:654 , HOH B:676 , HOH B:764 , HOH B:893 , ILE E:545 , HOH E:663BINDING SITE FOR RESIDUE GAL B 291
06AC6SOFTWAREASN B:255 , GAL B:291 , HOH B:917 , THR D:446 , HOH D:848 , ILE E:545BINDING SITE FOR RESIDUE BGC B 292
07AC7SOFTWARETHR C:331 , ASN C:332 , ARG C:333 , PHE C:363 , SER C:364 , GAL C:391 , HOH C:638 , HOH C:639 , ASP D:416 , HOH D:634BINDING SITE FOR RESIDUE GLA C 390
08AC8SOFTWAREHOH A:836 , THR C:354 , ASN C:355 , GLY C:362 , GLA C:390 , BGC C:392 , HOH C:639 , HOH C:825 , HOH C:895 , HOH C:941BINDING SITE FOR RESIDUE GAL C 391
09AC9SOFTWAREGLU A:128 , ASN C:355 , GAL C:391 , HOH C:639 , HOH C:664 , HOH C:895 , HOH C:898 , HOH C:964 , HOH E:823BINDING SITE FOR RESIDUE BGC C 392
10BC1SOFTWAREHOH A:722 , HOH B:756 , THR D:431 , ASN D:432 , ARG D:433 , GLY D:462 , PHE D:463 , SER D:464 , GAL D:491 , HOH D:734 , ASP E:516BINDING SITE FOR RESIDUE GLA D 490
11BC2SOFTWAREILE B:245 , HOH B:732 , HOH B:756 , HOH B:776 , THR D:454 , ASN D:455 , GLY D:462 , GLA D:490 , BGC D:492 , HOH D:697 , HOH D:728BINDING SITE FOR RESIDUE GAL D 491
12BC3SOFTWARETHR A:146 , HOH A:695 , ILE B:245 , ASN D:455 , GAL D:491 , HOH D:715 , HOH D:852 , HOH D:857 , HOH D:900BINDING SITE FOR RESIDUE BGC D 492
13BC4SOFTWAREASP A:116 , HOH A:783 , THR E:531 , ASN E:532 , ARG E:533 , GLY E:562 , PHE E:563 , SER E:564 , GAL E:591 , HOH E:681 , HOH E:706BINDING SITE FOR RESIDUE GLA E 590
14BC5SOFTWARETHR E:554 , ASN E:555 , GLY E:562 , GLA E:590 , BGC E:592 , HOH E:656 , HOH E:681 , HOH E:833 , HOH E:907 , HOH E:914BINDING SITE FOR RESIDUE GAL E 591
15BC6SOFTWAREGLU C:328 , ASN E:555 , GAL E:591 , HOH E:640 , HOH E:681 , HOH E:833BINDING SITE FOR RESIDUE BGC E 592

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:104 -A:157
2B:204 -B:257
3C:304 -C:357
4D:404 -D:457
5E:504 -E:557

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1C4Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 1C4Q)

(-) 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:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH19    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qa_ A: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qA00 A:101-169  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q A 101 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 169
                                   110       120       130       140       150       160         


Chain A from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH30    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qa_ A: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qA00 A:101-169  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q A 101 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 169
                                   110       120       130       140       150       160         


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH19    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qb_ B: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qB00 B:201-269  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q B 201 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 269
                                   210       220       230       240       250       260         


Chain B from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH30    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qb_ B: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qB00 B:201-269  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q B 201 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 269
                                   210       220       230       240       250       260         


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH19    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qc_ C: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qC00 C:301-369  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q C 301 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 369
                                   310       320       330       340       350       360         


Chain C from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH30    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qc_ C: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qC00 C:301-369  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q C 301 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 369
                                   310       320       330       340       350       360         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH19    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qd_ D: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qD00 D:401-469  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q D 401 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 469
                                   410       420       430       440       450       460         


Chain D from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH30    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qd_ D: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qD00 D:401-469  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q D 401 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 469
                                   410       420       430       440       450       460         


Chain E from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH19 | P69179 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH19    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qe_ E: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qE00 E:501-569  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q E 501 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 569
                                   510       520       530       540       550       560         


Chain E from PDB  Type:PROTEIN  Length:69
 aligned with STXB_BPH30 | P69178 from UniProtKB/Swiss-Prot  Length:89

    Alignment length:69
                                    30        40        50        60        70        80         
           STXB_BPH30    21 TPDCVTGKVEYTKYNDDDTFTVKVGDKELFTNRWNLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR  89
               SCOP domains d1c4qe_ E: Verotoxin-1/shiga-toxin, B-pentamer                        SCOP domains
               CATH domains 1c4qE00 E:501-569  [code=2.40.50.70, no name defined]                 CATH domains
               Pfam domains --------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeeeeee.....eeeee..eeeee..hhhhhhhhhhhhh..eeeee...........eeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------- Transcript
                 1c4q E 501 TPDCVTGKVEYTKYNDDDTFTVKVGDKELATNRANLQSLLLSAQITGMTVTIKTNACHNGGGFSEVIFR 569
                                   510       520       530       540       550       560
   Legend:   → Mismatch (orange background)
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    → 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  (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 1C4Q)

(-) Gene Ontology  (3, 6)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (STXB_BPH30 | P69178)
biological process
    GO:0019836    hemolysis by symbiont of host erythrocytes    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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.

Chain A,B,C,D,E   (STXB_BPH19 | P69179)
biological process
    GO:0019836    hemolysis by symbiont of host erythrocytes    The cytolytic destruction of red blood cells, with the release of intracellular hemoglobin, in the host organism by a symbiont. The host is defined as the larger of the organisms involved in a symbiotic interaction.
    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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  1c4q
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  STXB_BPH19 | P69179
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  STXB_BPH30 | P69178
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 Related Entries

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

UniProtKB/Swiss-Prot
        STXB_BPH19 | P69179: 1bos 1c48 1cqf 1czg 1czw 1d1i 1d1k 1ojf 1qnu 2c5c 2xsc 4ull
        STXB_BPH30 | P69178: 1bos 1c48 1cqf 1czg 1czw 1d1i 1d1k 1ojf 2c5c 2xsc 4ull

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1C4Q)