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 PERIPLASMIC DOMAIN OF TOLR FROM H. INFLUENZAE WITH SAXS DATA
 
Authors :  L. M. Parsons, A. Bax, A. Grishaev
Date :  15 Oct 07  (Deposition) - 01 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A,B  (20x)
Keywords :  Protein, Periplasmic Domain, Membrane, Inner Membrane, Protein Transport, Transmembrane, Transport, Membrane Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. M. Parsons, A. Grishaev, A. Bax
The Periplasmic Domain Of Tolr From Haemophilus Influenzae Forms A Dimer With A Large Hydrophobic Groove: Nmr Solution Structure And Comparison To Saxs Data.
Biochemistry V. 47 3131 2008
PubMed-ID: 18269247  |  Reference-DOI: 10.1021/BI702283X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN TOLR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21-STAR-(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: PERIPLASMIC DOMAIN
    Gene: TOLR
    Organism Scientific: HAEMOPHILUS INFLUENZAE
    Organism Taxid: 727
    Other Details: THE VECTOR WAS MODIFIED TO INCLUDE A NATIVE E.COLI GST-TAG.

 Structural Features

(-) Chains, Units

  
NMR Structure (20x): 

Summary Information (see also Sequences/Alignments below)

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

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

(-) Sites  (0, 0)

(no "Site" information available for 2JWL)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 2JWL)

(-) 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:74
 aligned with TOLR_HAEIN | P43769 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:74
                                    66        76        86        96       106       116       126    
           TOLR_HAEIN    57 DKVPVILEVAGIGKYAISIGGERQEGLTEEMVTQLSRQEFDKDNNTLFLVGGAKEVPYEEVIKALNLLHLAGIK 130
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeee.....eeeee..eeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2jwl A  19 GSVPVILEVAGIGKYAISIGGERQEGLTEEMVTQLSRQEFDKDNNTLFLVGGAKEVPYEEVIKALNLLHLAGIK  92
                                    28        38        48        58        68        78        88    


Chain B from PDB  Type:PROTEIN  Length:74
 aligned with TOLR_HAEIN | P43769 from UniProtKB/Swiss-Prot  Length:139

    Alignment length:74
                                    66        76        86        96       106       116       126    
           TOLR_HAEIN    57 DKVPVILEVAGIGKYAISIGGERQEGLTEEMVTQLSRQEFDKDNNTLFLVGGAKEVPYEEVIKALNLLHLAGIK 130
               SCOP domains -------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --ExbD-2jwlB01 B:21-92                                                     Pfam domains (1)
           Pfam domains (2) --ExbD-2jwlB02 B:21-92                                                     Pfam domains (2)
         Sec.struct. author ....eeeee.....eeeee..eeeeeehhhhhhhhhhhhhhhh....eeeee....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------- Transcript
                 2jwl B  19 GSVPVILEVAGIGKYAISIGGERQEGLTEEMVTQLSRQEFDKDNNTLFLVGGAKEVPYEEVIKALNLLHLAGIK  92
                                    28        38        48        58        68        78        88
   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 2JWL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (1, 2)

NMR Structure
(-)
Clan: no clan defined [family: ExbD] (2)

(-) Gene Ontology  (6, 6)

NMR Structure(hide GO term definitions)
Chain A,B   (TOLR_HAEIN | P43769)
molecular function
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

 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 2jwl)
 
  Sites
(no "Sites" information available for 2jwl)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2jwl)
 

(-) 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
  2jwl
    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
  TOLR_HAEIN | P43769
    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
  TOLR_HAEIN | P43769
    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
        TOLR_HAEIN | P43769: 2jwk

(-) Related Entries Specified in the PDB File

2jwk NO SAXS