Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - model 1
NMR Structure - model 1  (Jmol Viewer)
Image NMR Structure - all models
NMR Structure - all models  (Jmol Viewer)

(-) Description

Title :  SOLUTION STRUCTURE OF THE ALPHA SUBDOMAIN OF THE MAJOR NON-REPEAT UNIT OF FAP1 FIMBRIAE OF STREPTOCOCCUS PARASANGUIS
 
Authors :  S. Ramboarina, J. A. Garnett, A. Bodey, P. Simpson, B. Bardiaux, M. Nilg S. Matthews
Date :  17 Feb 10  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Helical Bundle, Cell Wall, Peptidoglycan-Anchor, Structural Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ramboarina, J. A. Garnett, M. Zhou, Y. Li, Z. Peng, J. D. Taylor, W. C. Lee, A. Bodey, J. W. Murray, Y. Alguel, J. Bergeron, B. Bardiaux, E. Sawyer, R. Isaacson, C. Tagliaferri, E. Cota, M. Nilges, P. Simpson T. Ruiz, H. Wu, S. Matthews
Structural Insights Into Serine-Rich Fimbriae From Gram-Positive Bacteria.
J. Biol. Chem. 2010
PubMed-ID: 20584910  |  Reference-DOI: 10.1074/JBC.M110.128165

(-) Compounds

Molecule 1 - FIMBRIAE-ASSOCIATED PROTEIN FAP1
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector: PRSETA
    Expression System Vector Type: VECTOR
    Fragment: UNP RESIDUES 196-276
    Gene: FAP1
    Organism Scientific: STREPTOCOCCUS PARASANGUINIS
    Organism Taxid: 1318
    Strain: FW213

 Structural Features

(-) Chains, Units

  
NMR Structure (10x): 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 2KUB)

(-) Sites  (0, 0)

(no "Site" information available for 2KUB)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2KUB)

(-) Sequences/Alignments

NMR Structure
   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:81
 aligned with FAP1_STRPA | A1C3L3 from UniProtKB/Swiss-Prot  Length:2587

    Alignment length:81
                                   222       232       242       252       262       272       282       292 
           FAP1_STRPA   213 ENLDKMISEAEVLNDMAARKLITLDAEQQLELMKSLVATQSQLEATKNLIGDPNATVADLQIAYTTLGNNTQALGNELIKL 293
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 2kub A 128 ENLDKMISEAEVLNDMAARKLITLDAEQQLELMKSLVATQSQLEATKNLIGDPNATVADLQIAYTTLGNNTQALGNELIKL 208
                                   137       147       157       167       177       187       197       207
   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  (0, 0)

(no "SCOP Domain" information available for 2KUB)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2KUB)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2KUB)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (FAP1_STRPA | A1C3L3)
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:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0009289    pilus    A proteinaceous hair-like appendage on the surface of bacteria ranging from 2-8 nm in diameter.

 Visualization

(-) Interactive Views

NMR Structure
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
(no "Ligands, Modified Residues, Ions" information available for 2kub)
 
  Sites
(no "Sites" information available for 2kub)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2kub)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ NMR Structure - model 1 PNG format | NMR Structure - all models PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  2kub
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  FAP1_STRPA | A1C3L3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  FAP1_STRPA | A1C3L3
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        FAP1_STRPA | A1C3L3: 2x12 3rgu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2KUB)