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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF S.EPIDERMIDIS ADHESIN SDRG BINDING TO FIBRINOGEN (ADHESIN-LIGAND COMPLEX)
 
Authors :  K. Ponnuraj, M. G. Bowden, S. Davis, S. Gurusiddappa, D. Moore, D. Choe, Y. Xu, M. Hook, S. V. L. Narayana
Date :  23 Sep 03  (Deposition) - 28 Oct 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.86
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Sdrg, Mscramm-Ligand Complex, Sdrg-Fibrinopeptide Complex, Cell Adhesion (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Ponnuraj, M. G. Bowden, S. Davis, S. Gurusiddappa, D. Moore, D. Choe, Y. Xu, M. Hook, S. V. L. Narayana
A "Dock, Lock And Latch" Structural Model For A Staphylococcal Adhesin Binding To Fibrinogen
Cell(Cambridge, Mass. ) V. 115 217 2003
PubMed-ID: 14567919  |  Reference-DOI: 10.1016/S0092-8674(03)00809-2
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FIBRINOGEN-BINDING PROTEIN SDRG
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: SDRG LIGAND BINDING A-DOMAIN
    Gene: SDRG
    Organism Scientific: STAPHYLOCOCCUS EPIDERMIDIS
    Organism Taxid: 1282
    Synonym: STAPHYLOCOCCUS EPIDERMIDIS ADHESIN SDRG
 
Molecule 2 - FIBRINOPEPTIDE B
    Chains: C, D
    Engineered: YES
    Other Details: THE PEPTIDE WAS CHEMICALLY SYNTHESIZED. THE SEQUENCE OF THE PEPTIDE (NEEGFFFSARGHRPLD) IS HOMOLOGOUS TO HUMAN FIBRINOGEN B BETA CHAIN 6-20
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1CA2Ligand/IonCALCIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU B:292 , SER B:297 , ILE B:300 , GLU B:307 , HOH B:637BINDING SITE FOR RESIDUE CA B 599
2AC2SOFTWAREGLU A:292 , SER A:297 , ILE A:300 , GLU A:307 , HOH A:673BINDING SITE FOR RESIDUE CA A 599

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R17)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R17)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R17)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R17)

(-) Exons   (0, 0)

(no "Exon" information available for 1R17)

(-) Sequences/Alignments

Asymmetric 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:321
 aligned with SDRG_STAEP | Q9KI13 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:321
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595 
           SDRG_STAEP   276 GSNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNTIAFSTSSGQGQGDLPP 596
               SCOP domains d1r17a1 A:276-424 Fibrinogen-binding adhesin SdrG                                                                                                    d1r17a2 A:425-596 Fibrinogen-binding adhesin SdrG                                                                                                                            SCOP domains
               CATH domains 1r17A01 A:276-424,A:583-596  [code=2.60.40.1280, no name defined]                                                                                    1r17A02 A:425-582  [code=2.60.40.1290, no name defined]                                                                                                       1r17A01        CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhh.eeeeeeeeee.......eee.hhh..eeeeeeeee........eeeee....ee............eee....eeeeeeee....eeeeee.hhhhh.eeeeeeeee..ee.........eeeeeeeee..eeeeeeeeee....eee..eeeeeeeeeee....eeeeeeee......eeeeeeeee..............eeeeee..............hhhhhee..hhh.eee....eeeeeeeee...eeeeeeee......hhhh.eeeeeeeee.......eeeeeeeeeeeee..eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r17 A 276 GSNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNTIAFSTSSGQGQGDLPP 596
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595 


Chain B from PDB  Type:PROTEIN  Length:320
 aligned with SDRG_STAEP | Q9KI13 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:320
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595
           SDRG_STAEP   276 GSNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNTIAFSTSSGQGQGDLP 595
               SCOP domains d1r17b1 B:276-424 Fibrinogen-binding adhesin SdrG                                                                                                    d1r17b2 B:425-595 Fibrinogen-binding adhesin SdrG                                                                                                                           SCOP domains
               CATH domains 1r17B01 B:276-424,B:583-595  [code=2.60.40.1280, no name defined]                                                                                    1r17B02 B:425-582  [code=2.60.40.1290, no name defined]                                                                                                       1r17B01       CATH domains
           Pfam domains (1) -----------------------------------------------------------------------------------------------------------------------------------------------------SdrG_C_C-1r17B01 B:425-583                                                                                                                                     ------------ Pfam domains (1)
           Pfam domains (2) -----------------------------------------------------------------------------------------------------------------------------------------------------SdrG_C_C-1r17B02 B:425-583                                                                                                                                     ------------ Pfam domains (2)
         Sec.struct. author ...hhh.eeeeeeeeee.......eee.hhh..eeeeeeeee........eeeee....ee............eee....eeeeeeee....eeeeee.hhhhh.eeeeeeeeeeeee.........eeeeeeeee..eeeeeeeeee....eee..eeeeeeeeeee....eeeeeeee......eeeeeeeee..............eeeeee..............hhhhhee..hhh.eee....eeeeeeeee...eeeeeeee......hhhh.eeeeeeeee.......eeeeeeeeeeeee..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r17 B 276 GSNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNTIAFSTSSGQGQGDLP 595
                                   285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595


Chain C from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1r17 C   8 GFFFSARGHRP  18
                                    17 


Chain D from PDB  Type:PROTEIN  Length:11
                                           
               SCOP domains ----------- SCOP domains
               CATH domains ----------- CATH domains
               Pfam domains ----------- Pfam domains
         Sec.struct. author ..eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------- SAPs(SNPs)
                    PROSITE ----------- PROSITE
                 Transcript ----------- Transcript
                 1r17 D   8 GFFFSARGHRP  18
                                    17
   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, 4)

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

(-) CATH Domains  (2, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: no clan defined [family: SdrG_C_C] (5)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (SDRG_STAEP | Q9KI13)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    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:0005618    cell wall    The rigid or semi-rigid envelope lying outside the cell membrane of plant, fungal, most prokaryotic cells and some protozoan parasites, maintaining their shape and protecting them from osmotic lysis. In plants it is made of cellulose and, often, lignin; in fungi it is composed largely of polysaccharides; in bacteria it is composed of peptidoglycan; in protozoan parasites such as Giardia species, it's made of carbohydrates and proteins.
    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.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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 Related Entries

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        SDRG_STAEP | Q9KI13: 1r19 2ral

(-) Related Entries Specified in the PDB File

1r19