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(-) Description

Title :  CRYSTAL STRUCTURE OF THE A-SUBUNIT OF THE AB5 TOXIN FROM E. COLI WITH NEU5GC-2,3GAL-1,3GLCNAC
 
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 :  2.10
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  (6, 25)

Asymmetric/Biological Unit (6, 25)
No.NameCountTypeFull Name
11PE5Ligand/IonPENTAETHYLENE GLYCOL
2AZI4Ligand/IonAZIDE ION
3GAL4Ligand/IonBETA-D-GALACTOSE
4NGA4Ligand/IonN-ACETYL-D-GALACTOSAMINE
5NGC4Ligand/Ion3,5-DIDEOXY-5-[(HYDROXYACETYL)AMINO]-D-GLYCERO-ALPHA-D-GALACTO-NON-2-ULOPYRANOSONIC ACID
6POL4Ligand/IonN-PROPANOL

(-) Sites  (20, 20)

Asymmetric Unit (20, 20)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:10 , PHE A:11 , SER A:12 , GLN A:36 , TYR A:78 , HOH A:134 , HOH A:135 , HOH A:139 , HOH A:143 , HOH A:184BINDING SITE FOR RESIDUE NGC A 127
02AC2SOFTWAREHOH A:146 , HOH A:184BINDING SITE FOR RESIDUE GAL A 128
03AC3SOFTWARETHR A:107 , GLU A:108 , HOH A:146BINDING SITE FOR RESIDUE NGA A 129
04AC4SOFTWAREGLY C:9 , MET C:10 , PHE C:11 , SER C:12 , GLN C:36 , TYR C:78 , HOH C:140 , HOH C:141 , HOH C:236 , HOH C:239BINDING SITE FOR RESIDUE NGC C 127
05AC5SOFTWAREASN B:26 , HOH C:214BINDING SITE FOR RESIDUE GAL C 128
06AC7SOFTWAREGLY D:9 , MET D:10 , PHE D:11 , SER D:12 , GLN D:36 , TYR D:78 , LYS D:115 , HOH D:135 , HOH D:137BINDING SITE FOR RESIDUE NGC D 127
07AC8SOFTWAREHOH D:135BINDING SITE FOR RESIDUE GAL D 128
08AC9SOFTWARETHR D:107 , GLU D:108BINDING SITE FOR RESIDUE NGA D 129
09BC1SOFTWAREASP E:8 , GLY E:9 , MET E:10 , PHE E:11 , SER E:12 , GLN E:36 , TYR E:78 , HOH E:160 , HOH E:171 , HOH E:180 , HOH E:246 , HOH E:250BINDING SITE FOR RESIDUE NGC E 127
10BC2SOFTWAREHOH E:138 , HOH E:171 , HOH E:181 , HOH E:246BINDING SITE FOR RESIDUE GAL E 128
11BC3SOFTWARETRP C:2 , GLY C:4 , ASP C:5 , ALA C:6 , HOH C:160 , TYR D:85 , PRO D:87 , THR E:107 , HOH E:181 , HOH E:182 , HOH E:215BINDING SITE FOR RESIDUE NGA E 129
12BC5SOFTWAREGLU A:108 , HOH A:182BINDING SITE FOR RESIDUE AZI A 131
13BC6SOFTWARETYR A:66 , THR A:69 , THR A:70 , TYR C:68 , THR C:69BINDING SITE FOR RESIDUE 1PE A 132
14BC7SOFTWAREASN B:62 , TYR B:66BINDING SITE FOR RESIDUE 1PE B 127
15BC9SOFTWAREHOH C:238BINDING SITE FOR RESIDUE AZI C 131
16CC3SOFTWARETYR D:66BINDING SITE FOR RESIDUE 1PE D 132
17CC4SOFTWARETHR C:69 , LEU D:65 , HOH D:141BINDING SITE FOR RESIDUE 1PE D 133
18CC5SOFTWAREASP C:5 , ALA C:6BINDING SITE FOR RESIDUE POL E 130
19CC6SOFTWAREARG C:7 , HOH C:145 , GLU E:108 , HOH E:136BINDING SITE FOR RESIDUE AZI E 131
20CC7SOFTWARETYR E:66 , THR E:69BINDING SITE FOR RESIDUE 1PE E 132

(-) SS Bonds  (9, 9)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3DWQ)

(-) 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 ..........................eeeeeeeee.................hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwq 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 ..........................eeeeeeeee.................hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwq 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 ..........................eeeeeeeee.................hhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee.................. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dwq 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 ..........................eeeeeeeee...............hhhhhhhhhhhhhhhhhhhhh.eeeeeee.....hhhhhhhh...eeeeeee............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwq 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 ..........................eeeeeeeee.................hhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhh...eeeeeee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------- Transcript
                 3dwq 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 3DWQ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) 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
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  3dwq
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  Q3ZTX8_ECOLX | Q3ZTX8
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 Related Entries

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

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

(-) Related Entries Specified in the PDB File

3dwa 3dwp