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 :  DER F 2, THE MAJOR MITE ALLERGEN FROM DERMATOPHAGOIDES FARINAE, NMR, 10 STRUCTURES
 
Authors :  S. Ichikawa, H. Hatanaka, T. Yuuki, N. Iwamoto, K. Ogura, Y. Okumura, F. Inagaki
Date :  07 Apr 97  (Deposition) - 08 Apr 98  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (10x)
Keywords :  Allergen, Immunoglobulin Fold (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Ichikawa, H. Hatanaka, T. Yuuki, N. Iwamoto, S. Kojima, C. Nishiyama, K. Ogura, Y. Okumura, F. Inagaki
Solution Structure Of Der F 2, The Major Mite Allergen For Atopic Diseases.
J. Biol. Chem. V. 273 356 1998
PubMed-ID: 9417088  |  Reference-DOI: 10.1074/JBC.273.1.356
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DER F 2
    Cellular Location: EXTRACELLULAR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PFLT1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Common: AMERICAN HOUSE DUST MITE
    Organism Scientific: DERMATOPHAGOIDES FARINAE
    Organism Taxid: 6954
    Synonym: DER F II

 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 1AHM)

(-) Sites  (0, 0)

(no "Site" information available for 1AHM)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:8 -A:119
2A:21 -A:27
3A:73 -A:78

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

NMR Structure (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_ALL2_DERFA_001 *M93VALL2_DERFA  ---  ---AV76V
2UniProtVAR_ALL2_DERFA_002 *I105AALL2_DERFA  ---  ---AI88A
3UniProtVAR_ALL2_DERFA_003 *I128VALL2_DERFA  ---  ---AI111V
4UniProtVAR_ALL2_DERFA_004 *G142AALL2_DERFA  ---  ---AG125A
   * ID not provided by source
  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1AHM)

(-) 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:129
 aligned with ALL2_DERFA | Q00855 from UniProtKB/Swiss-Prot  Length:146

    Alignment length:129
                                    27        37        47        57        67        77        87        97       107       117       127       137         
           ALL2_DERFA    18 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFMKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 146
               SCOP domains d1ahma_ A: Major mite allergen                                                                                                    SCOP domains
               CATH domains 1ahmA00 A:1-129  [code=2.60.40.770, no name defined]                                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee....eeeeeee................eeeeeeee.....eeeeeeeee....eeee...................eeeeeeee...........eeeeeeee....eeeeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------V-----------A----------------------V-------------A---- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ahm A   1 DQVDVKDCANNEIKKVMVDGCHGSDPCIIHRGKPFTLEALFDANQNTKTAKIEIKASLDGLEIDVPGIDTNACHFVKCPLVKGQQYDIKYTWNVPKIAPKSENVVVTVKLIGDNGVLACAIATHGKIRD 129
                                    10        20        30        40        50        60        70        80        90       100       110       120
   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 1AHM)

(-) Gene Ontology  (1, 1)

NMR Structure(hide GO term definitions)
Chain A   (ALL2_DERFA | Q00855)
cellular component
    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.

 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 1ahm)
 
  Sites
(no "Sites" information available for 1ahm)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1ahm)
 

(-) 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
  1ahm
    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
  ALL2_DERFA | Q00855
    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
  ALL2_DERFA | Q00855
    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
        ALL2_DERFA | Q00855: 1ahk 1wrf 1xwv 2f08

(-) Related Entries Specified in the PDB File

1ahk