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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STAPHYLOCOCCAL SUPERANTIGEN-LIKE PROTEIN SSL5 AT PH 4.6 COMPLEXED WITH SIALYL LEWIS X
 
Authors :  H. M. Baker, I. Basu, M. C. Chung, T. Caradoc Davies, J. D. Fraser, E. N. B
Date :  06 Sep 07  (Deposition) - 27 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Ob Fold, B-Grasp, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. M. Baker, I. Basu, M. C. Chung, T. Caradoc-Davies, J. D. Fraser, E. N. Baker
Crystal Structures Of The Staphylococcal Toxin Ssl5 In Complex With Sialyl Lewis X Reveal A Conserved Binding Site That Shares Common Features With Viral And Bacterial Sialic Acid Binding Proteins
J. Mol. Biol. V. 374 1298 2007
PubMed-ID: 17996251  |  Reference-DOI: 10.1016/J.JMB.2007.09.091

(-) Compounds

Molecule 1 - EXOTOXIN 3
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A.3C
    Expression System Strain: AD494
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 31-234
    Gene: SSL5
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: GL10
    Synonym: SUPERANTIGEN-LIKE PROTEIN SSL5

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 6)

Asymmetric/Biological Unit (6, 6)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3GOL1Ligand/IonGLYCEROL
4NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
5PO41Ligand/IonPHOSPHATE ION
6SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:137 , TYR A:173 , TYR A:174 , THR A:175 , ARG A:186 , ASP A:189 , GAL A:602 , NAG A:603 , HOH A:644 , HOH A:658 , HOH A:716BINDING SITE FOR RESIDUE SIA A 601
2AC2SOFTWAREASP A:104 , TYR A:105 , GLN A:183 , HIS A:185 , ARG A:186 , SIA A:601 , GAL A:602 , FUC A:604BINDING SITE FOR RESIDUE NAG A 603
3AC3SOFTWAREGLU A:177 , GLN A:183 , ARG A:186 , SIA A:601 , NAG A:603 , FUC A:604 , HOH A:640 , HOH A:657BINDING SITE FOR RESIDUE GAL A 602
4AC4SOFTWAREGLU A:177 , LYS A:180 , GLN A:183 , GAL A:602 , NAG A:603 , HOH A:659 , HOH A:688BINDING SITE FOR RESIDUE FUC A 604
5AC5SOFTWAREASP A:74 , LYS A:97 , ASN A:98 , HOH A:651BINDING SITE FOR RESIDUE PO4 A 605
6AC6SOFTWAREHIS A:128 , TYR A:131 , LYS A:132 , VAL A:135 , GLU A:139 , LEU A:140 , LYS A:143 , HOH A:664BINDING SITE FOR RESIDUE GOL A 606

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2Z8L)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2Z8L)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2Z8L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2Z8L)

(-) Exons   (0, 0)

(no "Exon" information available for 2Z8L)

(-) 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:192
 aligned with Q9ZFS6_STAAU | Q9ZFS6 from UniProtKB/TrEMBL  Length:234

    Alignment length:192
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232  
         Q9ZFS6_STAAU    43 DIFDLRDYYSRASKELKNVTGYRYSKGGKHYLIFDKNRKFTRIQIFGKDIERIKKRKNPGLDIFVVKEAENRNGTVYSYGGVTKKNQGAYYDYLSAPRFVIKKEVGAGVSVHVKRYYIYKEEISLKELDFKLRQYLIQDFDLYKKFPKASKIKVTMKDGGYYTFELNKKLQTNRMSDVIDGRNIEKIEANIR 234
               SCOP domains d2z8la1 A:13-100 Superantigen-like protein SET3                                         d2z8la2 A:101-204 Superantigen-like protein SET3                                                         SCOP domains
               CATH domains 2z8lA01   2z8lA02 A:23-97  [code=2.40.50.110, no name defined]                       2z8lA01 A:13-22,A:98-204  [code=3.10.20.120, no name defined]                                               CATH domains
               Pfam domains --DUF1954-2z8lA02 A:15-98                                                             ------------Stap_Strp_tox_C-2z8lA01 A:111-204                                                              Pfam domains
         Sec.struct. author hhhhhhhhhh...eeeeeeeeeeeee..eeeeeeee..eeeeeee..hhhhhh...eeeeeeeee...ee.....eeee..eee.............eeeeeeee..eeeeeeee......eeehhhhhhhhhhhhhhhh..........eeeeee....eeeee.....hhhhh..eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2z8l A  13 DIFDLRDYYSGASKELKNVTGYRYSKGGKHYLIFDKHQKFTRIQIFGKDIERLKTRKNPGLDIFVVKEAENRNGTVFSYGGVTKKNQGAYYDYLNAPKFVIKKEVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYKKFPKDSKIKVIMKDGGYYTFELNKKLQPHRMSDVIDGRNIEKMEANIR 204
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202
   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  (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: DUF1954] (9)

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q9ZFS6_STAAU | Q9ZFS6)
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/TrEMBL
        Q9ZFS6_STAAU | Q9ZFS6: 1m4v 2r61

(-) Related Entries Specified in the PDB File

1m4v SSL5
2r61 SSL5 COMPLEXED WITH SIALYL LEWIS X AT PH 7.4