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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS OF S.EPIDERMIDIS ADHESIN SDRG BINDING TO FIBRINOGEN (APO STRUCTURE)
 
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 :  3.51
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Mscramm, Sdrg Native, 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, C, D
    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: STAPHYLOCOCCAL EPIDERMIDIS ADHESIN SDRG

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1R19)

(-) Sites  (0, 0)

(no "Site" information available for 1R19)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1R19)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1R19)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1R19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1R19)

(-) Exons   (0, 0)

(no "Exon" information available for 1R19)

(-) 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:286
 aligned with SDRG_STAEP | Q9KI13 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:304
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576    
           SDRG_STAEP   277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNT 580
               SCOP domains d1r19a1 A:277-424 Fibrinogen-binding adhesin Sd  rG                                                                                                 d1r19a2 A:425-580 Fibrinogen-binding adhesin SdrG                                                                                                            SCOP domains
               CATH domains 1r19A01 A:277-424  [code=2.60.40.1280, no name   defined]                                                                                           1r19A02 A:425-580  [code=2.60.40.1290, no name defined]                                                                                                      CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeeee.......ee.......eeeeeeeee......--.eeee....ee........-..ee.---....eeeeee....eeeee-hhhhh---.eeeeeeeeeee.........eee..eeee..eeee..eee.....eee..eeeeeeeeeee....eeeeeeee......eeeeeeeee..............eeeeee..............hhhhhee..hhh.eee.--.eeeeeeeee...eeeeeeee...------...eeeeeeee.......eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r19 A 277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKS--TMTVNIDKNTVPSDLTDSF-IPKIK---GEIIATGTYDNTNKQITYT-TDYVD---NIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLG--NDVNINFGNIDSPYIIKVISKYDP------TIQQTVTMQTTINEYTGEFRTASYDNT 580
                                   286       296       306       316      |326       336       346   |   356       366     | 376 |   | 386       396       406       416       426       436       446       456       466       476       486       496       506       516    |  526       536       546|      556       566       576    
                                                                        323  |               344 | 350 354               372 | 378 382                                                                                                                                        521  |                    547    554                          
                                                                           326                 346                         374                                                                                                                                                   524                                                        


Chain B from PDB  Type:PROTEIN  Length:300
 aligned with SDRG_STAEP | Q9KI13 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:308
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576        
           SDRG_STAEP   277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNTIAFS 584
               SCOP domains d1r19b1 B:277-424 Fibrinogen-binding adhesin Sdr G                                                                                                  d1r19b2 B:425-584 Fibrinogen-binding adhesin SdrG                                                                                                                SCOP domains
               CATH domains 1r19B01 B:277-424,B:583-584  [code=2.60.40.1280,  no name defined]                                                                                  1r19B02 B:425-582  [code=2.60.40.1290, no name defined]                                                                                                       1r CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh...eeeeee.......eee......eeeeeeee........-eeeee....ee............ee.....eeeeeee.....eeeeee.-----....eeeeeeeeee.........eeeeeeeee..eeeeeeeeee....eee..eeeeeeeeeee....eeeeeeee......eeeeeeeee..............eeeeee..............hhhhhee..hhh.eee....eeeeeeeee...eeeeeeee.....--.eeeeeeeeeeee.......eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r19 B 277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSG-TMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFT-----YENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNK--YTTIQQTVTMQTTINEYTGEFRTASYDNTIAFS 584
                                   286       296       306       316       326       336       346       356       366       | -   |   386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546  |  | 556       566       576        
                                                                         324 |                                             374   380                                                                                                                                                                      549  |                                
                                                                           326                                                                                                                                                                                                                               552                                


Chain C from PDB  Type:PROTEIN  Length:298
 aligned with SDRG_STAEP | Q9KI13 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:308
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576        
           SDRG_STAEP   277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNTIAFS 584
               SCOP domains d1r19c1 C:277-424 Fibrinogen-binding adhesin Sdr G                                                                                                  d1r19c2 C:425-584 Fibrinogen-binding adhesin SdrG                                                                                                                SCOP domains
               CATH domains 1r19C01 C:277-424,C:583-584  [code=2.60.40.1280,  no name defined]                                                                                  1r19C02 C:425-582  [code=2.60.40.1290, no name defined]                                                                                                       1r CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhh.eeeeeeeeee.......eee.hhh..eeeeeeeee.......-.eeee....ee............ee...--eeeeee......eeeee.----......eeeeeeeeee.........eeeeeeeee..eeeeeeeeee....eee..eeeeeeeeeee....eeeeeeee......eeeeeeeee..............eeeeee..............hhhhhee..hhh.eee....eeeeeeeee...eeeeeeee....---..eeeeeeeeeee.......eeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r19 C 277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSG-TMTVNIDKNTVPSDLTDSFAIPKIKDNS--IIATGTYDNTNKQITYTF----DKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPN---YTTIQQTVTMQTTINEYTGEFRTASYDNTIAFS 584
                                   286       296       306       316       326       336       346      |356       366      |  - |     386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546 |   | 556       566       576        
                                                                         324 |                        353  |              373  378                                                                                                                                                                       548 552                                
                                                                           326                           356                                                                                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:292
 aligned with SDRG_STAEP | Q9KI13 from UniProtKB/Swiss-Prot  Length:931

    Alignment length:310
                                   286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586
           SDRG_STAEP   277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDSFAIPKIKDNSGEIIATGTYDNTNKQITYTFTDYVDKYENIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISKYDPNKDDYTTIQQTVTMQTTINEYTGEFRTASYDNTIAFSTS 586
               SCOP domains d1r19d1 D:277-424 Fibrinogen-binding adhesin SdrG                                                                                                   d1r19d2 D:425-586 Fibrinogen-binding adhesin SdrG                                                                                                                  SCOP domains
               CATH domains 1r19D01 D:277-424,D:583-586  [code=2.60.40.1280, no name defined]                                                                                   1r19D02 D:425-582  [code=2.60.40.1290, no name defined]                                                                                                       1r19 CATH domains
           Pfam domains (1) -------------------------------------------------------------------  ------   ------------------ -----   -------------------------------------------SdrG_C_C-1r19D01 D:425-583                                                                                                                                     --- Pfam domains (1)
           Pfam domains (2) -------------------------------------------------------------------  ------   ------------------ -----   -------------------------------------------SdrG_C_C-1r19D02 D:425-583                                                                                                                                     --- Pfam domains (2)
           Pfam domains (3) -------------------------------------------------------------------  ------   ------------------ -----   -------------------------------------------SdrG_C_C-1r19D03 D:425-583                                                                                                                                     --- Pfam domains (3)
           Pfam domains (4) -------------------------------------------------------------------  ------   ------------------ -----   -------------------------------------------SdrG_C_C-1r19D04 D:425-583                                                                                                                                     --- Pfam domains (4)
         Sec.struct. author ..hhh.eeeee..eee.......eee......eeeeeeeee.........eeee....ee.......--......---.....eeee....eeee.-.....---.eeeeeeeeeee.........eeeeee.ee..eeeeeeeeee....eee..eeeeeeeeeee....eeeeeeee......eeeeeeeee..............eeeeee..............hhhhhee..hhh.eee....eeeeeeeee...eeeeeee.--------.eeeeeeeeeee...-...eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1r19 D 277 SNVNHLIKVTDQSITEGYDDSDGIIKAHDAENLIYDVTFEVDDKVKSGDTMTVNIDKNTVPSDLTDS--IPKIKD---EIIATGTYDNTNKQITYT-TDYVD---NIKAHLKLTSYIDKSKVPNNNTKLDVEYKTALSSVNKTITVEYQKPNENRTANLQSMFTNIDTKNHTVEQTIYINPLRYSAKETNVNISGNGDEGSTIIDDSTIIKVYKVGDNQNLPDSNRIYDYSEYEDVTNDDYAQLGNNNDVNINFGNIDSPYIIKVISK--------TTIQQTVTMQTTINE-TGEFRTASYDNTIAFSTS 586
                                   286       296       306       316       326       336      |346    |  356       366     | 376 |   | 386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       | -      |556       566| |    576       586
                                                                                            343  |  351 355              372 | 378 382                                                                                                                                                               544      553           567 |                 
                                                                                               346                         374                                                                                                                                                                                                569
   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, 8)

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

(-) CATH Domains  (2, 8)

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

(-) Pfam Domains  (1, 4)

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

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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

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

UniProtKB/Swiss-Prot
        SDRG_STAEP | Q9KI13: 1r17 2ral

(-) Related Entries Specified in the PDB File

1r17