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 ANTHERAEA POLYPHEMUS PHEROMONE BINDING PROTEIN (APOLPBP)
 
Authors :  S. Mohanty, S. Zubkov, A. M. Gronenborn
Date :  03 Sep 03  (Deposition) - 23 Mar 04  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Pheromone Binding Protein, Antheraea Polyphemus, Pbp, Apolpbp, Hexahelical Fold, Pbp Fold, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mohanty, S. Zubkov, A. M. Gronenborn
The Solution Nmr Structure Of Antheraea Polyphemus Pbp Provides New Insight Into Pheromone Recognition By Pheromone-Binding Proteins
J. Mol. Biol. V. 337 443 2004
PubMed-ID: 15003458  |  Reference-DOI: 10.1016/J.JMB.2004.01.009
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PHEROMONE-BINDING PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PHN1+
    Expression System Strain: XA-90
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: POLYPHEMUS MOTH
    Organism Scientific: ANTHERAEA POLYPHEMUS
    Organism Taxid: 7120
    Synonym: PBP

 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 1QWV)

(-) Sites  (0, 0)

(no "Site" information available for 1QWV)

(-) SS Bonds  (3, 3)

NMR Structure
No.Residues
1A:19 -A:54
2A:50 -A:108
3A:97 -A:117

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 1QWV)

(-) 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:142
 aligned with PBP_ANTPO | P20797 from UniProtKB/Swiss-Prot  Length:163

    Alignment length:142
                                    31        41        51        61        71        81        91       101       111       121       131       141       151       161  
            PBP_ANTPO    22 SPEIMKNLSNNFGKAMDQCKDELSLPDSVVADLYNFWKDDYVMTDRLAGCAINCLATKLDVVDPDGNLHHGNAKDFAMKHGADETMAQQLVDIIHGCEKSAPPNDDKCMKTIDVAMCFKKEIHKLNWVPNMDLVIGEVLAEV 163
               SCOP domains d1qwva_ A: Moth pheromone-binding protein, PBP                                                                                                 SCOP domains
               CATH domains 1qwvA00 A:1-142  [code=1.10.238.20, no name defined]                                                                                           CATH domains
               Pfam domains PBP_GOBP-1qwvA01 A:1-123                                                                                                   ------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhh.hhhhhhhhhh.hhhhhhhhh..........hhhhhhhhhhhhhhhh.........hhhhhhhhhhh..hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhh................ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1qwv A   1 SPEIMKNLSNNFGKAMDQCKDELSLPDSVVADLYNFWKDDYVMTDRLAGCAINCLATKLDVVDPDGNLHHGNAKDFAMKHGADETMAQQLVDIIHGCEKSAPPNDDKCMKTIDVAMCFKKEIHKLNWVPNMDLVIGEVLAEV 142
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140
   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 alpha proteins (14657)

(-) CATH Domains  (1, 1)

NMR Structure
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: no clan defined [family: PBP_GOBP] (36)

(-) Gene Ontology  (4, 4)

NMR Structure(hide GO term definitions)
Chain A   (PBP_ANTPO | P20797)
molecular function
    GO:0005549    odorant binding    Interacting selectively and non-covalently with an odorant, any substance capable of stimulating the sense of smell.
    GO:0005550    pheromone binding    Interacting selectively and non-covalently with a pheromone, a substance, or characteristic mixture of substances, that is secreted and released by an organism and detected by a second organism of the same or a closely related species, in which it causes a specific reaction, such as a definite behavioral reaction or a developmental process.
biological process
    GO:0019236    response to pheromone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a pheromone stimulus.
    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 1qwv)
 
  Sites
(no "Sites" information available for 1qwv)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1qwv)
 

(-) 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
  1qwv
    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
  PBP_ANTPO | P20797
    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
  PBP_ANTPO | P20797
    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
        PBP_ANTPO | P20797: 1two 2jpo

(-) Related Entries Specified in the PDB File

1ls8 NMR STRUCTURE OF THE UNLIGANDED BOMBYX MORI PHEROMONE- BINDING PROTEIN AT PHYSIOLOGICAL PH