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(-) Description

Title :  CRYSTAL STRUCTURE OF YERSINIA PSEUDOTUBERCULOSIS-DERIVED MITOGEN (YPM)
 
Authors :  R. Donadini, C. W. Liew, A. H. Kwan, J. P. Mackay, B. A. Fields
Date :  09 Jun 03  (Deposition) - 27 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Jelly Roll Fold, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Donadini, C. W. Liew, A. H. Kwan, J. P. Mackay, B. A. Fields
Crystal And Solution Structures Of A Superantigen From Yersinia Pseudotuberculosis Reveal A Jelly-Roll Fold.
Structure V. 12 145 2004
PubMed-ID: 14725774  |  Reference-DOI: 10.1016/J.STR.2003.12.002
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - YPM
    Chains: A, B, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMAL-P2X
    Expression System Strain: NOVABLUE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: YPMA
    Organism Scientific: YERSINIA PSEUDOTUBERCULOSIS
    Organism Taxid: 633

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 1PM4)

(-) Sites  (0, 0)

(no "Site" information available for 1PM4)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:32 -A:129
2B:32 -B:129
3C:32 -C:129

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PM4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1PM4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1PM4)

(-) Exons   (0, 0)

(no "Exon" information available for 1PM4)

(-) 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:117
 aligned with Q57221_YERPU | Q57221 from UniProtKB/TrEMBL  Length:151

    Alignment length:117
                                    44        54        64        74        84        94       104       114       124       134       144       
         Q57221_YERPU    35 IPNIATYTGTIQGKGEVCIIGNKEGKTRGGELYAVLHSTNVNADMTLILLRNVGGNGWGEIKRNDIDKPLKYEDYYTSGLSWIWKIKNNSSETSNYSLDATVHDDKEDSDVLTKCPV 151
               SCOP domains d1pm4a_ A: Superantigen (mitogen) Ypm                                                                                 SCOP domains
               CATH domains 1pm4A00 A:15-131 Superantigen (mitogen) Ypm                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeee........eeeeeeee.......eeeeeeee....eeeeeeeee....eeeeeee.....eeeeeee.....eeeeeeee.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm4 A  15 IPNIATYTGTIQGKGEVCIIGNKEGKTRGGELYAVLHSTNVNADMTLILLRNVGGNGWGEIKRNDIDKPLKYEDYYTSGLSWIWKIKNNSSETSNYSLDATVHDDKEDSDVLTKCPV 131
                                    24        34        44        54        64        74        84        94       104       114       124       


Chain B from PDB  Type:PROTEIN  Length:117
 aligned with Q57221_YERPU | Q57221 from UniProtKB/TrEMBL  Length:151

    Alignment length:117
                                    44        54        64        74        84        94       104       114       124       134       144       
         Q57221_YERPU    35 IPNIATYTGTIQGKGEVCIIGNKEGKTRGGELYAVLHSTNVNADMTLILLRNVGGNGWGEIKRNDIDKPLKYEDYYTSGLSWIWKIKNNSSETSNYSLDATVHDDKEDSDVLTKCPV 151
               SCOP domains d1pm4b_ B: Superantigen (mitogen) Ypm                                                                                 SCOP domains
               CATH domains 1pm4B00 B:15-131 Superantigen (mitogen) Ypm                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeee........eeeeeeee.......eeeeeee.....eeeeeeeee....eeeee.......eeeeeee.....eeeeeeee.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm4 B  15 IPNIATYTGTIQGKGEVCIIGNKEGKTRGGELYAVLHSTNVNADMTLILLRNVGGNGWGEIKRNDIDKPLKYEDYYTSGLSWIWKIKNNSSETSNYSLDATVHDDKEDSDVLTKCPV 131
                                    24        34        44        54        64        74        84        94       104       114       124       


Chain C from PDB  Type:PROTEIN  Length:117
 aligned with Q57221_YERPU | Q57221 from UniProtKB/TrEMBL  Length:151

    Alignment length:117
                                    44        54        64        74        84        94       104       114       124       134       144       
         Q57221_YERPU    35 IPNIATYTGTIQGKGEVCIIGNKEGKTRGGELYAVLHSTNVNADMTLILLRNVGGNGWGEIKRNDIDKPLKYEDYYTSGLSWIWKIKNNSSETSNYSLDATVHDDKEDSDVLTKCPV 151
               SCOP domains d1pm4c_ C: Superantigen (mitogen) Ypm                                                                                 SCOP domains
               CATH domains 1pm4C00 C:15-131 Superantigen (mitogen) Ypm                                                                           CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee....eeeeee.......eeeeeeeee.......eeeeeeee.....eeeeeeee....eeeeeee.....eeeeeee.....eeeeeeee.....hhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------- Transcript
                 1pm4 C  15 IPNIATYTGTIQGKGEVCIIGNKEGKTRGGELYAVLHSTNVNADMTLILLRNVGGNGWGEIKRNDIDKPLKYEDYYTSGLSWIWKIKNNSSETSNYSLDATVHDDKEDSDVLTKCPV 131
                                    24        34        44        54        64        74        84        94       104       114       124
   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  (1, 3)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 3)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1PM4)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 1PM4)

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  1pm4
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  Q57221_YERPU | Q57221
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 Related Entries

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

UniProtKB/TrEMBL
        Q57221_YERPU | Q57221: 1poq

(-) Related Entries Specified in the PDB File

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