Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)NMR Structure - manually
(-)NMR Structure - model 1
(-)NMR Structure - all models
collapse expand < >
Image NMR Structure - manually
NMR Structure - manually  (Jmol Viewer)
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 DER F 13, GROUP 13 ALLERGEN FROM HOUSE DUST MITES
 
Authors :  S. L. Chan, Y. K. Mok
Date :  16 Jun 05  (Deposition) - 11 Apr 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Beta Barrel, Helix, Allergen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. L. Chan, S. T. Ong, S. Y. Ong, F. T. Chew, Y. K. Mok
Nuclear Magnetic Resonance Structure-Based Epitope Mapping And Modulation Of Dust Mite Group 13 Allergen As A Hypoallergen.
J. Immunol. V. 176 4852 2006
PubMed-ID: 16585580
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DER F 13
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-M
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: AMERICAN HOUSE DUST MITE
    Organism Scientific: DERMATOPHAGOIDES FARINAE
    Organism Taxid: 6954

 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 2A0A)

(-) Sites  (0, 0)

(no "Site" information available for 2A0A)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2A0A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2A0A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2A0A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2A0A)

(-) Exons   (0, 0)

(no "Exon" information available for 2A0A)

(-) 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:131
 aligned with Q1M2P5_DERFA | Q1M2P5 from UniProtKB/TrEMBL  Length:131

    Alignment length:131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130 
         Q1M2P5_DERFA     1 MASIEGKYKLEKSEKFDEFLDKLGVGFMVKTAAKTLKPTFEVAIENDQYIFRSLSTFKNTEAKFKLGEEFEEDRADGKRVKTVIQKEGDNKFVQTQFGDKEVKIIREFNGDEVVVTASCDGVTSVRTYKRI 131
               SCOP domains d2a0aa1 A:1-131 Der f 13 allergen                                                                                                   SCOP domains
               CATH domains 2a0aA00 A:1-131  [code=2.40.128.20, no name defined]                                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee....hhhhhhhhhh.hhhhhhhhhh...eeeeee....eeeee......eeeee.....eeeee...eeeeeeeeee...eeeeee.....eeeeeee...eeeeeee....eeeeeeeee Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2a0a A   1 MASIEGKYKLEKSEKFDEFLDKLGVGFMVKTAAKTLKPTFEVAIENDQYIFRSLSTFKNTEAKFKLGEEFEEDRADGKRVKTVIQKEGDNKFVQTQFGDKEVKIIREFNGDEVVVTASCDGVTSVRTYKRI 131
                                    10        20        30        40        50        60        70        80        90       100       110       120       130
   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, 1)

NMR Structure
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2A0A)

(-) Gene Ontology  (3, 3)

NMR Structure(hide GO term definitions)
Chain A   (Q1M2P5_DERFA | Q1M2P5)
molecular function
    GO:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    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: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.

 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 2a0a)
 
  Sites
(no "Sites" information available for 2a0a)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2a0a)
 

(-) 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
  2a0a
    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
  Q1M2P5_DERFA | Q1M2P5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  Q1M2P5_DERFA | Q1M2P5
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2A0A)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2A0A)