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(-) Description

Title :  CRYSTAL STRUCTURE OF THE STAPHYLOCOCCAL SUPERANTIGEN-LIKE PROTEIN SSL5 IN COMPLEX WITH SIALYL-LEWIS X AT PH 7.4
 
Authors :  H. M. Baker
Date :  05 Sep 07  (Deposition) - 27 Nov 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Ssl5, Superantigen-Like, Sialyl Lewis X, Sialic Acid Binding, Chips, 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 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  (7, 7)

Asymmetric/Biological Unit (7, 7)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4GOL1Ligand/IonGLYCEROL
5NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
6SIA1Ligand/IonO-SIALIC ACID
7SRT1Ligand/IonS,R MESO-TARTARIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:27 , LEU A:28 , LYS A:29 , VAL A:31 , LEU A:137 , TYR A:173 , TYR A:174 , THR A:175 , ARG A:186 , ASP A:189 , GAL A:602 , HOH A:661 , HOH A:662 , HOH A:663BINDING SITE FOR RESIDUE SIA A 601
2AC2SOFTWAREALA A:101 , LYS A:180 , GLN A:183 , HIS A:185 , ARG A:186 , GAL A:602 , FUC A:604 , HOH A:661BINDING SITE FOR RESIDUE NAG A 603
3AC3SOFTWAREASN A:30 , LYS A:180 , SIA A:601 , NAG A:603 , FUC A:604 , HOH A:662 , HOH A:663BINDING SITE FOR RESIDUE GAL A 602
4AC4SOFTWAREASN A:30 , LYS A:97 , GLU A:177 , LYS A:180 , GAL A:602 , NAG A:603BINDING SITE FOR RESIDUE FUC A 604
5AC5SOFTWARELYS A:110 , ARG A:127BINDING SITE FOR RESIDUE CL A 205
6AC6SOFTWAREARG A:35 , LEU A:65 , HIS A:124 , LYS A:126 , TYR A:147 , HOH A:630 , HOH A:634BINDING SITE FOR RESIDUE SRT A 206
7AC7SOFTWAREGLU A:116 , LYS A:160 , ASP A:161 , ASN A:202 , ARG A:204BINDING SITE FOR RESIDUE GOL A 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2R61)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2R61)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2R61)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2R61)

(-) Exons   (0, 0)

(no "Exon" information available for 2R61)

(-) 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:195
 aligned with Q9ZFS6_STAAU | Q9ZFS6 from UniProtKB/TrEMBL  Length:234

    Alignment length:197
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       
         Q9ZFS6_STAAU    38 ENVTKDIFDLRDYYSRASKELKNVTGYRYSKGGKHYLIFDKNRKFTRIQIFGKDIERIKKRKNPGLDIFVVKEAENRNGTVYSYGGVTKKNQGAYYDYLSAPRFVIKKEVGAGVSVHVKRYYIYKEEISLKELDFKLRQYLIQDFDLYKKFPKASKIKVTMKDGGYYTFELNKKLQTNRMSDVIDGRNIEKIEANIR 234
               SCOP domains d2r61a1 A:8-100 Superantigen-like protein SET3                                               d2r61a2 A:101-204 Superantigen-like protein SET3                                                         SCOP domains
               CATH domains 2r61A01        2r61A02 A:23-97  [code=2.40.50.110, no name defined]                       2r61A01 A:8-22,A:98-204  [code=3.10.20.120, no name defined]                                                CATH domains
               Pfam domains -------DUF1954-2r61A02 A:15-98                                                             ------------Stap_Strp_tox_C-2r61A01 A:111-204                                                              Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...eeeeeeeeeeee....eeee........eeeehhhhhh.....eeeeeeeee.......--..eee..eee.............eeeeeeee..eeeeeeee......eeehhhhhhhhhhhhhhhhh.........eeeeee....eeeee.....hhhhh..eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2r61 A   8 ENVTKDIFDLRDYYSGASKELKNVTGYRYSKGGKHYLIFDAHQAFTRIQIFGKDIERLKARKNPGLDIFVVKEAENR--TVFSYGGVTKKNQGAYYDYLNAPKFVIKKEVDAGVYTHVKRHYIYKEEVSLKELDFKLRQYLIQNFDLYKKFPKDSKIKVIMKDGGYYTFELNKKLQPHRMSDVIDGRNIEKMEANIR 204
                                    17        27        37        47        57        67        77      | 87        97       107       117       127       137       147       157       167       177       187       197       
                                                                                                       84 87
   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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  2r61
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 Related Entries

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

UniProtKB/TrEMBL
        Q9ZFS6_STAAU | Q9ZFS6: 1m4v 2z8l

(-) Related Entries Specified in the PDB File

1m4v SSL5
2z8l SSL5 COMPLEXED WITH SIALYL LEWIS X AT PH 4.6