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(-) Description

Title :  CRYSTAL STRUCTURE OF THE B-SUBUNIT OF THE AB5 TOXIN FROM E. COLI WITH NEU5GC
 
Authors :  E. Byres, A. W. Paton, J. C. Paton, J. C. Lofling, D. F. Smith, M. C. J. Wilce, U. M. Talbot, D. C. Chong, H. Yu, S. Huang, X. Chen, N. M. Varki, A. Varki, J. Rossjohn, T. Beddoe
Date :  22 Jul 08  (Deposition) - 04 Nov 08  (Release) - 09 Dec 08  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B,C,D,E
Keywords :  Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. Byres, A. W. Paton, J. C. Paton, J. C. Lofling, D. F. Smith, M. C. J. Wilce, U. M. Talbot, D. C. Chong, H. Yu, S. Huang, X. Chen, N. M. Varki, A. Varki, J. Rossjohn, T. Beddoe
Incorporation Of A Non-Human Glycan Mediates Human Susceptibility To A Bacterial Toxin
Nature V. 456 648 2008
PubMed-ID: 18971931  |  Reference-DOI: 10.1038/NATURE07428
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - SUBTILASE CYTOTOXIN, SUBUNIT B
    Chains: A, B, C, D, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: RESIDUES IN DATABASE 24-141
    Gene: SUBB
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: SUBB

 Structural Features

(-) Chains, Units

  12345
Asymmetric/Biological Unit : ABCDE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 10)

Asymmetric/Biological Unit (2, 10)
No.NameCountTypeFull Name
11PE5Ligand/IonPENTAETHYLENE GLYCOL
2NGC5Ligand/Ion3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONIC ACID

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:9 , MET A:10 , PHE A:11 , SER A:12 , GLN A:36 , SER A:40 , TYR A:78 , HOH A:206 , HOH A:211BINDING SITE FOR RESIDUE NGC A 127
02AC2SOFTWAREGLY B:9 , MET B:10 , PHE B:11 , SER B:12 , GLN B:36 , TYR B:78 , HOH B:201 , HOH B:205 , HOH B:206BINDING SITE FOR RESIDUE NGC B 127
03AC3SOFTWAREASP C:8 , GLY C:9 , MET C:10 , PHE C:11 , SER C:12 , GLN C:36 , TYR C:78 , LYS C:115 , HOH C:203 , HOH C:222BINDING SITE FOR RESIDUE NGC C 127
04AC4SOFTWAREASP D:8 , GLY D:9 , MET D:10 , PHE D:11 , SER D:12 , GLN D:36 , TYR D:78 , LYS D:115 , HOH D:273BINDING SITE FOR RESIDUE NGC D 127
05AC5SOFTWAREGLY E:9 , MET E:10 , PHE E:11 , SER E:12 , GLN E:36 , SER E:40 , TYR E:78 , LYS E:115 , HOH E:182 , HOH E:188 , HOH E:208BINDING SITE FOR RESIDUE NGC E 127
06AC6SOFTWAREASN A:62 , TYR A:66 , THR A:70 , 1PE C:128 , 1PE E:128BINDING SITE FOR RESIDUE 1PE A 128
07AC7SOFTWAREASN B:62 , TYR B:66 , THR B:70 , HOH B:174 , 1PE E:128 , HOH E:149BINDING SITE FOR RESIDUE 1PE B 128
08AC8SOFTWARE1PE A:128 , ASN C:62 , THR C:69 , HOH C:193 , 1PE D:128BINDING SITE FOR RESIDUE 1PE C 128
09AC9SOFTWARE1PE C:128 , ASN D:62 , TYR D:66 , THR D:69 , THR D:70 , HOH D:276BINDING SITE FOR RESIDUE 1PE D 128
10BC1SOFTWARE1PE A:128 , 1PE B:128 , TYR E:66BINDING SITE FOR RESIDUE 1PE E 128

(-) SS Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1A:31 -A:45
2A:103 -A:109
3B:31 -B:45
4B:103 -B:109
5C:31 -C:45
6C:103 -C:109
7D:31 -D:45
8D:103 -D:109
9E:31 -E:45
10E:103 -E:109

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Asp A:8 -Gly A:9
2Asp B:8 -Gly B:9
3Ser B:37 -Ala B:38
4Asp C:8 -Gly C:9
5Asp D:8 -Gly D:9
6Asp E:8 -Gly E:9

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DWP)

(-) 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:116
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:116
                                    33        43        53        63        73        83        93       103       113       123       133      
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKK 139
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeeee....eeeeeee.....hhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwp A   1 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKK 116
                                    10        20        30        40        50        60        70        80        90       100       110      


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:117
                                    33        43        53        63        73        83        93       103       113       123       133       
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 140
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwp B   1 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain C from PDB  Type:PROTEIN  Length:120
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:120
                                                                                                                                               141  
                                    33        43        53        63        73        83        93       103       113       123       133       | -
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKNS--   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dwp C   1 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKNSLE 120
                                    10        20        30        40        50        60        70        80        90       100       110       120


Chain D from PDB  Type:PROTEIN  Length:117
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:117
                                    33        43        53        63        73        83        93       103       113       123       133       
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 140
               SCOP domains --------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee....hhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwp D   1 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKKN 117
                                    10        20        30        40        50        60        70        80        90       100       110       


Chain E from PDB  Type:PROTEIN  Length:116
 aligned with Q3ZTX8_ECOLX | Q3ZTX8 from UniProtKB/TrEMBL  Length:141

    Alignment length:116
                                    33        43        53        63        73        83        93       103       113       123       133      
         Q3ZTX8_ECOLX    24 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKK 139
               SCOP domains -------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeeeeeeeeeeee..eeeeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwp E   1 EWTGDARDGMFSGVVITQFHTGQIDNKPYFCIEGKQSAGSSISACSMKNSSVWGASFSTLYNQALYFYTTGQPVRIYYEPGVWTYPPFVKALTSNALVGLSTCTTSTECFGPDRKK 116
                                    10        20        30        40        50        60        70        80        90       100       110
   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  (0, 0)

(no "SCOP Domain" information available for 3DWP)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DWP)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E   (Q3ZTX8_ECOLX | Q3ZTX8)
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.

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  Cis Peptide Bonds
    Asp A:8 - Gly A:9   [ RasMol ]  
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    Asp D:8 - Gly D:9   [ RasMol ]  
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    Ser B:37 - Ala B:38   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/TrEMBL
        Q3ZTX8_ECOLX | Q3ZTX8: 3dwa 3dwq 4bwg

(-) Related Entries Specified in the PDB File

3dwa 3dwq