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(-) Description

Title :  CRYSTAL STRUCTURE OF STAPHYLOCOCCAL SUPERANTIGEN-LIKE PROTEIN 11 IN COMPLEX WITH SIALYL LEWIS X
 
Authors :  M. C. Chung, B. D. Wines, H. Baker, R. J. Langley, E. N. Baker, J. D. Fraser
Date :  24 Sep 07  (Deposition) - 18 Dec 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Ob Fold, Beta Grasp, Protein-Carbohydrate Complex, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. C. Chung, B. D. Wines, H. Baker, R. J. Langley, E. N. Baker, J. D. Frase
The Crystal Structure Of Staphylococcal Superantigen-Like Protein 11 In Complex With Sialyl Lewis X Reveals The Mechanism For Cell Binding And Immune Inhibition
Mol. Microbiol. V. 66 1342 2007
PubMed-ID: 18045383  |  Reference-DOI: 10.1111/J.1365-2958.2007.05989.X

(-) Compounds

Molecule 1 - SUPERANTIGEN-LIKE PROTEIN 11
    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
    Gene: SSL11
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Strain: US6610

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2FUC1Ligand/IonALPHA-L-FUCOSE
3GAL1Ligand/IonBETA-D-GALACTOSE
4K3Ligand/IonPOTASSIUM ION
5NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
6SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:6 , GLN A:8 , GLN A:11 , LEU A:130 , PHE A:166 , TYR A:167 , THR A:168 , ARG A:179 , ASP A:182 , GAL A:602 , HOH A:623 , HOH A:646 , HOH A:649 , HOH A:721BINDING SITE FOR RESIDUE SIA A 601
2AC2SOFTWAREARG A:6 , HIS A:178 , ARG A:179 , GAL A:602 , FUC A:604 , HOH A:619 , HOH A:662 , HOH A:750 , HOH A:764 , HOH A:788 , HOH A:947BINDING SITE FOR RESIDUE NDG A 603
3AC3SOFTWAREARG A:6 , GLN A:11 , GLU A:170 , GLN A:176 , SIA A:601 , NDG A:603 , FUC A:604 , HOH A:623 , HOH A:630 , HOH A:649 , HOH A:676BINDING SITE FOR RESIDUE GAL A 602
4AC4SOFTWAREGLN A:11 , GLU A:170 , LYS A:173 , GAL A:602 , NDG A:603 , HOH A:662 , HOH A:697 , HOH A:704 , HOH A:768 , HOH A:802 , HOH A:903BINDING SITE FOR RESIDUE FUC A 604
5AC5SOFTWAREGLN A:99 , ASN A:100 , HOH A:664 , HOH A:832 , HOH A:859 , HOH A:944BINDING SITE FOR RESIDUE K A 605
6AC6SOFTWAREGLN A:8 , GLN A:11 , CIT A:608 , HOH A:649 , HOH A:676 , HOH A:854BINDING SITE FOR RESIDUE K A 606
7AC7SOFTWARESER A:108 , GLY A:110 , GLN A:111 , THR A:113 , HOH A:752BINDING SITE FOR RESIDUE K A 607
8AC8SOFTWAREGLN A:8 , ARG A:91 , THR A:92 , HIS A:94 , LYS A:156 , ARG A:158 , K A:606 , HOH A:806 , HOH A:821 , HOH A:841 , HOH A:854 , HOH A:902BINDING SITE FOR RESIDUE CIT A 608

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser A:74 -Gly A:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2RDG)

(-) 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 A8E1U5_STAAU | A8E1U5 from UniProtKB/TrEMBL  Length:196

    Alignment length:192
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194  
         A8E1U5_STAAU     5 VRSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
               SCOP domains d2rdga1 A:5-93 automated matches                                                         d2rdga2 A:94-196 automated matches                                                                      SCOP domains
               CATH domains 2rdgA01       2rdgA02 A:19-89  [code=2.40.50.110, no name defined]                   2rdgA01 A:5-18,A:90-196  [code=3.10.20.120, no name defined]                                                CATH domains
               Pfam domains ------DUF1954-2rdgA02 A:11-90                                                         --------Stap_Strp_tox_C-2rdgA01 A:99-196                                                                   Pfam domains
         Sec.struct. author ..hhhhhhhhhhhh..eeeeeeeeeeee..eeeeee..eeeeee...hhhhhh..eeeeeeeeeee......hhhhhee..eee..........eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhh..........eeeeee....eeeee.....hhhhh..eee...eeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2rdg A   5 VRSQATQDLSEYYNRPYFDLRNLSGYREGNTVTFINHYQQTDVKLEGKDKDKIKDGNNENLDVFVVREGSGRQADNNSIGGITKTNRTQHIDTVQNVNLLVSKSTGQHTTSVTSTNYSIYKEEISLKELDFKLRKHLIDKHDLYKTEPKDSKIRVTMKNGDFYTFELNKKLQTHRMGDVIDGRNIEKIEVNL 196
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194
   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   (A8E1U5_STAAU | A8E1U5)
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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  Cis Peptide Bonds
    Ser A:74 - Gly A:75   [ RasMol ]  
 

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